I'm wrapping up 100% right now, and I've got a few impressions:
The game's alright. It's a lot of fun. It's still got some big problems, and it's not as good as prime, but I would like to see them take another crack at this formula.
However: They really, really need 3 people next time:
1) Someone who can actually write dialogue
2) Someone who really gets level design and pacing
3) Someone who can make catchy tunes
That second one is the most important of the bunch. They give you this character that's really fun to control, but there aren't that many cool rooms to go nuts in. My biggest problem with this game isn't the story, it's the level design and pacing.
Didn't mind the controls (thought they were pretty neat, still needed optional nunchuck support though), game has good graphics (character design is surprisingly good for a Team Ninja game), don't like the ambient soundtrack. I like the garbage time bit after the ending, but really the exploration needs to be integrated into the game instead of being some optional thing.
The story has some really good ideas with some really dodgy execution. Same goes for characterization. Speaking of that:

: You know...despite some really cheesy dialogue and weird moments, I like her a lot more after this game.
She reminds me a lot of Iron Man actually, the comic version. Other M was half "goddamn, you're a professional, you gotta handle things better than this" and half "goddamn, she is
awesome". Tony Stark is the only other character I've seen with those kinds of highs and lows. The similarities between the two characters are a little eerie.
Didn't really like the depressed Samus you spent most of the game playing as, but everything about her after the Sector Zero scene is great. I hope
that's who we play as from now on.
This is corny, but I like that she was actually a pretty friendly and humble person, at least when she wasn't having a meltdown. Looking back, those two traits make a lot of sense. Didn't like that she was humble to a fault, but thankfully in Fusion she's humble to a point

.

: With the way they go on and on about this guy you'd think he'd be Captain America, Optimus Prime and Roy Fokker rolled up into one. He isn't, and that's a big problem with this game's story. A really, really big problem. At worst he's a dick and a control freak for no reason, and at best he's just...there.

Awesome. Metroid really needed a character like this. It's weird how this story fucks up with with Adam in nearly every way, but totally nails this guy.