I've ranted about Other M countless times. My disappointment with the game is well known. But, and I emphasize this, I do feel that Other M was born out of great ideas that just plain fell apart with bad execution. Fundamental issues, both story and gameplay, that prior games did so WELL are either ignored or forgotten about in this game.
I also tell people I am an avid video game designer myself. Creating games, good games, is not just an ambition, it is my career, and something I've had to dedicate myself to mastering. I'm no master, mind you, but I do think I've got the chops for it.
Mainly, I use the Art of Game Design as my bible for development.

For everything I think Other M did wrong, as a game, I would like to say what I'd have done to make it better.
This is about to get heavy... just warning ya.
GRAPHICS
By most accounts, Other M is one of the best-looking games on the system... technically. The models have a lot of detail and could offer a lot of animation and expression, and the world and creatures are competently made.
But there's a huge problem, and it's a problem my modeling instructors taught me in my first quarter of class. When you create something, anything, create it with "history". Nothing in reality is clean and pristine and perfect; it has wear and tear, dirt and scratches and dents and rust and chipped paint...
Everything in Other M is far too "clean". Soldiers' armor looks fresh off the assembly line. Walls are smooth and plain. Everything looks like it was created in a computer; it looks fake. Compare that to other games, from Bioshock to Halo to Arkham City, any game with a smidgen of "realism", and you see armor with peeling paint and scratches, walls with smudges and dirt and grime, environments that looked lived in, characters that look weathered, and creatures that seem natural to those environments. Other M, technically, is good... but there is so little history, so few special touches, that it's visuals are sterile and bland. Adding those special little touches would've gone a long way.
SOUND
I know I'm not alone here, but a lot of the old-school Metroid sound effects were disappointingly missing. That's not exactly reason enough to be upset, but it does tie into a phrase from the book I mentioned that stuck with me: "Nintendo games excel at giving players auditory cues to let them know they're doing well: the sound of Mario growing taller, the sound of Link opening a chest and obtaining an item, the sound of Samus acquiring an upgrade."
Other M was strangely lacking in the special sounds department. Even ambient noise was rather limited, let alone all those special touches (again) that make great games great. I recently played Batman: Arkham City, Skyward Sword, Spirit Tracks, and Deus Ex: Human Revolution to test this theory out, but I noticed all of those games have dynamic sound. As you play the game, the audio cues the games give you shift and change in subtle ways to let you know whether you're playing well or not. They're subtle, almost subliminal, but if you heard someone playing these games and heard only the sounds, not even voices or music, you'd know how the person playing was faring.
Other M, by comparison, was almost stifling in its own quiet way, as if it didn't want sounds to detract from the experience... but even playing a game like Metroid Prime, I'm reminded of the way Samus's breath would fill my ears, the way steam would hiss and spray on my visor, of the way doors would unlock, switches would be flipped, scans would be found, shots would hit or miss, timers would activate, map and health stations would unlock, upgrades would be acquired, and even how the beam cannon sounded when you shifted to a new weapon to fire. The sound effects were brilliant, yet Other M's were lacking those little extra touches.
MUSIC
Not to be confused with the sound effects, which are intrinsically tied to direct gameplay, the score of a game is just as important as setting a mood... just as the absence of music can convey a similar sense of isolation and loneliness.
Other M had some huge, orchestral Hollywood-level pomp during certain scenes, but for most of the game it was awkwardly lacking. And that's... okay. I attest that the early-to-mid Silent Hill games are masterpieces of atmospheric melodies that are stirring and effective when you hear them... and MORE effect when you're not even aware they're there... or when they've stopped playing and let the world speak for itself.
The problem wasn't that, it was just that music was put to such poor use in Other M. Many areas are silent that would've thrived with a melodic tether, akin to the phenomenal Phenandra Drifts, Torvus Bog, Skytown, or even as far back as the eerie NES original or the alternative heroic/chilling Gameboy scores. Alternatively, many scenes filled with high-end bombastic music would've benefited far more with much less. Mentioning Silent Hill again, in SH2, there's a scene with an elevator that was one of the most gut-wrenching scenes in any medium ever... movie, game, comic... and the music that played was a simple, quiet, almost childish melody that went up, then down, then up, then down..... that was it, and it was effective.
I don't need a huge orchestra for a Metroid game. I don't even need a score, really. But I would also say that those long, boring, bland jogs down empty, bland hallways would've been more interesting if the music existed to inspire and spur me forward.
PUZZLES
In the Art of Game Design, there's an entire chapter dedicated to puzzles and the battle of "heads" vs. "hands". Puzzles have been one of Metroid's strengths since the first game, tasking players with finding the right weapon or upgrade to progress pass previously impassable walls and barriers. Recent games have thrived on morph ball puzzles, or even puzzle-laden boss battles. But in the chapter I read, there was also big, bold risks: "Puzzles must be readily understood, they must serve both gameplay and narrative purposes, they must not be too easy as to be boring nor too difficult as to cause players frustration, and the player must enjoy analyzing a puzzle, the act of solving the puzzle, and the reward given for solving it."
Other M fails hard at this.
You could argue that the puzzles themselves, in general, took a backseat to the combat, but what does exist is poorly implemented. Look back at what I read, I can name puzzles of the game that violated all those rules. How many of us had the "puzzle" of trying to figure out where to go, got lost, and realized the game meant for us to run to a dead-end for no reason only to turn around and backtrack so that we could trigger a cutscene? How many utterly pointless pixel-hunts ground our enjoyment of the game to jolting halt and forced us to tiresomely look at dull smears for over ten minutes? How many times was our "reward" nothing more than a long-winded cutscene or, at times, nothing at all, making it nothing more than wasted filler that expected "solving the puzzle" to be the only reward in and of itself?
I would have either tied the puzzles to story and gameplay better ("You need to solve this puzzle to restore air to the ship before we suffocate!" "You need to turn down the heat in this sector before our heat shields give out!" "You need to restore power to this part of the ship by finding these missing components!"), I would have made the rewards for doing so much more satisfying (Prime games often gave very worthwhile and necessary expansions and upgrades), or I would have just cut many of them out entirely (pixel-hunts mostly).
COMBAT
Okay, so this game was action-heavy, with those Team Ninja fellas at the helm. Great combat, right? Lots of flashy moves and...
... And most of the combat boiled down to "mindlessly hit the fire button, let it auto-aim, then hit the finisher command". Rinse, repeat. It was actually, in my opinion, regressive. Compare this to a series like the Zelda franchise. Skyward Sword requires very particular focus and attention to aim your sword down the vulnerable section of an enemy. You have to be aware of not just your own abilities, but the enemy as well is ever-changing to your tactics and forces you to alter yours to come out on top.
I've had problems with the Prime games too, mind you. Strafe, strafe, fire, strafe, roll out of attack range, fire, strafe, strafe. But Other M is just as bad, only it really had a much higher pedigree from its developers to aspire towards.
Let's focus on Team Ninja's own "Ninja Gaiden". I've played it. Hard as nails. I hate the difficulty to the extreme, but I won't ever argue that their combat system isn't top-notch. Every enemy has a weakness, a "tell" sign. You have to find it, learn it, and master the correct counter-measure to take against even the lowliest of enemies. You have to know which enemies to fight in the air, which to fight at a distance, which to fight up close, which to separate from groups, which to dispatch in groups, whether to use shurikens, arrows, magic spells, swords, lances, claws, scythes... there was so much variety, but you had to do TWO things: master your own skills and master reading and countering the skills of every enemy.
Other M's combat, by comparison, is beyond rudimentary. I remember when people feared the Prime series would become a mindless button-mashing shooter, but enemies in Prime were pretty smart. Some couldn't even be damaged by normal shots. Many were invincible on the front and needed to be stunned in the back. Some needed you to go into morph ball mode and damage them on the inside with bombs. Other M had a few of them, but for every one unique enemy that tested your skills, you were met with room after room where you just needed to fire and auto-aim could kill them before you even saw them pop up on screen. It was shallow, and the scripted instant-kills she could do were flashy, but they served no gameplay reason (and in fact could be argued to run counter to her "weak" portrayal in the story).
LEVEL DESIGN
How many invisible walls were in this game? How many empty hallways? How many pointless dead-ends? How many sterile labs? How many token elemental areas were there? Granted, this all took place on one (stupidly-named) ship, but the variety of levels was wholly generic. There was not a single level in the game that wasn't done in a prior game, and done better, either in design, mood, pacing, atmosphere, or personality. The ice level was no Phanandra Drifts, the laval level no Magmoor's Cavern, the labs, even, paled in comparison to Metroid Fusion. There was nothing wholly-original; it was very much a retread of Zebes, which is great for some cheap nostalgia, but I'm willing to venture people would've preferred something entirely new, bold, and exciting.
Zelda games routinely take place in vastly different landscapes, even if they share similar climates: Wind Waker is covered with oceans, yet it's nothing like Majora's Mask's Great Bay or Spirit Track's Ocean Realm. A Link to the Past's Lost Woods is hardly similar to Ocarina of Time's or Twilight Princess's. They shift and change and mutate into new worlds that keep the essentials of the old yet manifest themselves in entirely new forms and creative, lush designs and details. Beyond that, the manner of getting across these different, even similar, areas changes game-to-game; by a boat with a sail whose winds you yourself control, by horse, by train, by bird, by magic teleporting songs, by foot, by snowboard (loved the Yeti race), by long-jumps, by kangaroo, by bear, by dinosaur, by wolf form, by rabbit form, by Goron form, by Zora form, by Deku form...
Samus used to keep pace with Link in that regard. Morph ball, plasma beam, dash boots, shinesparking, screw attacking. But she's since STOPPED, pretty much dead in her tracks after Super Metroid. By limiting Samus's abilities to the same abilities she has had in the past and offering nothing more, the levels themselves only function in the same way we've seen them traversed before. Can you imagine a new power-up that lets you phase through certain doors (or enemies) like a ghost? Or an upgrade that lets you fire your ice beam at slopes and allows you to slide across the floor to reach new areas? Imagine if you were in a magnetic environment where you had new positive-and-negative beams or upgrades you had to fire or activate and disable to solve puzzles or to just make it through the level without being stuck to the floor? New, original, fun ways of traveling through the Metroid world.
Other M needed levels that demanded that. Something new. Something fun. Something fresh and memorable to give the game a personality and charm all its own, rather than decided to play it safe and retread decades-old ground.
WEAPON SYSTEM
Going back to the Art of Game Design, one of the foundational game rules in that book is "as the player plays the game, keep their interest by having them earn rewards that keeps them playing. A well-paced game continually empowers the player and makes them feel in control. Above all else, a player MUST feel in control of their own fate in the game."
Games like Super Mario Bros 3 empower the player. You break a brick, get a mushroom, get bigger, get a flower, get fire, and the game becomes easier. You earn more lives the better you play. You can endure longer, kill quicker, traverse levels easier... but all of this is by the player's OWN hands.
Zelda games often do this. You earn passageway into new areas by your own exploits. Dead-ends are eventually opened up by earning the appropriate item to open them. Bosses are felled by weapons you yourself discover. Even dungeon maps and compasses are items EARNED and not given, and they embolden and empower the player.
You know where I'm going with this. The "Authorization" system in Other M. Now, it's a good idea in theory to try something new, and if they had just been smarter about it it might even have worked. As is, it is the OPPOSITE of making the player feel in control. Weapons and upgrades are restored arbitrarily by Adam, which is already a gameplay sin, but Samus WILLINGLY de-empowers herself, a narrative sin and one that creates dissonance between avatar and player.
What I would have done, if I HAD to have this authorization system rather than "earning" upgrades, is I would have added a story mechanic that says that something on the ship activated an electro-magnetic pulse that has shut off all their weapons and armor systems. Adam volunteers to head to the control room to manually restore power. Then, at certain points in the game, Adam calls in to tell you he's succeeded in restoring "heat shield" functions or "you can probably use your grapple beam now" functions... This would 1) make Adam both useful AND a likeable ally that helps EMPOWER you rather than DEPOWER you and 2) would make the current system they used work in the game world, yet still make the player feel relief, not anger, once they realized a power was restored rather than "re-allowed".
STORY
The story. Oh boy. Oh boy oh boy.
The original poster said it best. "kill your darling." I read an interview at comic-con with Jim Lee (I think it was Jim Lee), where they asked him about a controversial decision he made and he was asked "don't you like this character? Why did you kill him off?" He responded (in gist), "I love these characters, but I must always distance myself from them. If I grow protective of them, I'll never take risks or go down new paths or do things that I feel would benefit the bigger picture. I want to be just as sad to see a character die as the reader, so to do that, as a creator, I must divorce myself from my protective feelings."
I will not pretend to know how Yoshio Sakamoto feels about Samus, but given his public statements about being protective of her, viewing her "as a daughter", jokingly saying she's his ideal woman and wishing she'd ask him out on a date, etc., I can tell he's someone that I feel doesn't know where to take Samus, or knows and decided to regress her instead of letting her boldly mature and evolve past his influence or understanding.
Samus means a lot of things to many people, but Other M gave most fans a completely different woman than the one we had seen in action before. I utterly reject the erroneous claims that "she had no personality before" or "this is the first time she had a voice", which all hardcore Metroid fans know to be incorrect, dating back to her speaking in Super Metroid & Fusion and her exhibiting very blatant and very memorable personality traits in nearly all prior games.
The folks from Extra Credits said it best: actions speak louder than words. We can deduce a great deal about Samus based on her behavior in-game (the mark of a good game character), her chosen occupation and the situations she throws herself into, and the way she handles herself in these situations. Metroid Prime 2 always stood out to me because, really, Samus has no personal reason to be there. Her ship was damaged, fine. She can just sit there and wait for it to be fixed. But, nope, she discovers a race of people in dire need of a hero to save them from darkness and evil. She dives into a mystery, overcomes great personal conflict and loss, and saves the day, becoming a legend to these creatures she barely knows and walks off into the light content with herself knowing that she did the best she could, all she could, when no one else was willing or able to lend a hand. I could write an entire thesis paper on her personality in that game, from the grand picture to the minutia of personal details in her body language to how she treats a dead soldier.
But the problems with Other M's story are well-known. The question: how would I improve it?
I'll be generic and encompassing.
1) Make the story ENHANCE the gameplay, not conflict with it. A good game uses story to support its gameplay, not hinder it. Other M's story got in the way of the game, often, in many ways. It gave us lengthy, unskippable cutscenes when we just wanted to play. Its reasons for events to happen destroyed players suspension of disbelief. It showed a certain Samus in cutscenes that was unlike the one in combat or solving puzzles. I can't really even name a single event, story-wise, in the game that made the GAME better.
2) Make the player CONNECT with the main heroine. After the Prime games literally put you behind Samus's visor, thinking, acting, BREATHING as her, Other M was especially jarring. But it was more jarring by constantly reminding the player that this was Samus's story, not THEIR story. They just moved her around, but the player, themselves, was just along for her ride, rather than making it his or her own personal Samus journey, to feel what she felt, to see what she saw, to think as she does, to struggle as she might. Samus constantly figures out things we already knew, repeats things we've already heard, tells us outright "what to feel" (I call this "Anakin Skywalker" syndrom... and it's terrible writing at its worst), and she, herself, seems entirely in the dark and dependent on everyone else around her, relying on others, rather than the PLAYERS, to help her understand and survive her ordeal.
I know I reference the Zelda games often (they're peerless in game design), but Link was called "Link" in the first game because he is the "link" between player and character on screen. A good game puts you in their shoes, makes YOU that character, be they Mario, Cloud, Master Chief, Link, Kratos, Batman, etc. Those games make you FEEL like those characters because they tap into the parts of ourselves we aspire to be. Other M Samus throws up a wall, a barrier, between what we want to be and what we want HER to be. Many people I know, even men, aspired to be like the Samus of old; few people I've spoken to feel any connection to her after Other M.
It's strange that the Prime games, despite having NO dialogue and very few cutscenes, created a bond and a passion between Samus and gamers that Other M's dialogue-heavy narrative and cutscene-laden script failed to do, even with its boastful "2 hour story mode". Sakamoto forgot the gaming principle that games thrive because they are "interactive" and they mean something to people because it is THEIR actions that cause the games interaction. I don't care about Samus's actions; I care about MY actions AS Samus.
3) Trim the fat. In my script-writing class, I was told this simple rule: "everything you write must have at least two reasons for being there. If not, cut it." Other M is full of bloat. So much wasted time is spent on characters we neither know nor care about (and the game doesn't care about them either, since most are killed off-screen). So much repetition of phrases and words. So much vague reminiscing and context-deprived encounters. It's odd that the game is so bloated, says so much over and over, yet it fails to answer vital questions about, say, the Ridley encounter or even make it clear what Samus and Adam's real relationship is. For the minor stuff, yeah, that's overflowing; but for the important stuff? Cryptic, vague half-answers at best. So much of the story would've been improved if the things that weren't working got scrapped (anybody going to miss the Deleter sub-plot? Anyone?) and things that needed real context got their due treatment (anybody going to mention the Chozo? Anyone?)
Lastly, the story failed on a cultural level. This is a personal bias, I admit, and people's tastes will vary, but I'll routinely groan anytime they mention Samus was picked on for "being a woman" when that was the LEAST interesting thing they could pick on her for. I'll groan about the whole "I'm a brat that thumbs down orders" when she used to follow every order as the Chozo trained her to do. I'll be disappointed by her sexualized portrayal with her running into combat in high-heels (I wear heels... no, no, no....), leering Zero-suit shots, and her having so many "emotional" girly melt-downs while the big, tough, stone-faced men scowl at her babbling and go about doing their jobs with fearless determination... the kind of determination I always saw her having in prior games (Prime 3 in particular has the military view her in the utmost respect and admiration due to how professional and effective she is.)
I would have seriously scrapped the plot almost in general, or at least found several highly professional and critical editors to go over it several more times. It was a poorly jumbled mess, and the game as a whole fails due to RELYING on that story to carry it through to the end. Granted, I say it was bad, but it did have some fantastic ideas in there at times (dealing with the aftermath of Super Metroid, the baby's sacrifice, tying up loose ends for Fusion).
My final rule though, again from the Art of Game Design, the Art Institute, and the lips of Shigeru Miyamoto, Sid Meier, and many others: "Gameplay comes FIRST". In Other M, it didn't. Not by a long shot. It wasn't bad, but the emphasis was not on making the best GAME possible, but rather on the story. It hurt. It hurt everything. The story did not mesh with the gameplay. The story dictated how the game was played and even contradicted the gameplay. The story got in the way of the player's enjoyment. It got in the way of rewarding and empowering the player. The story got in the way of everything a player might enjoy, from exploration to puzzle-solving to combat, because the story was there in the background, making our actions in the game confusing, conflicting, and cumbersome.
Gameplay MUST come first. It must. Say what you will about the Uncharted series, they know how to make a game. They even state they come up with wild ideas and action-events to play through FIRST and then make up excuses to fit them all together in a story. In Other M, it was the reverse. Story was written down and a game was adapted from it. That's not the way it should be. That's not the way the next game should be developed.
Gameplay first. If all my other "improvements" go ignored, fine, but gameplay MUST come first.
If you made it to the end, CONGRATS! You're awesome! You can have a cookie!

Thanks for reading!