After completing the game, I've only got a few complaints about it.
One thing that really bothered me was Li. The guy had as much depth as the dumbo squid pet. >.> I mean, he played the second banana role to the maximum extent of the phrase. Maybe it was because he had no voice, but he really felt tacked on. In all honesty, in retrospect, I wouldn't have minded of Naija had drowned the bastard in the cave with his Mr. T wannabe 'do. ;P
Another thing that roasts my muffins about this game is that aquatic text stuff scattered everywhere, I figured at some point you would be able to click them to have Naija read them, or even just hover it with yer mouse to have it change like on the title screen. But nope, here there's all this text everywhere that looks like it'd be important or interesting and it's completely lost to those who don't have a PhD in cryptography. =(
Finally, Naija has a distinct need to literally FLY out of suspended bubbles at high velocity no matter how slowly you move to their edge. Granted this only came into play at the Lobster boss... But it was still significant enough to be annoying. (Not that the bubble hopping acrossed the frozen veil wasn't annoying at times...)
That gets rid of the major stuff. Now onto the minor gripes.
I really think the dumbo octopus pet should've followed your cursor rather than Naija... Having the thing trail behind you most of the time basically wastes it. (Though I DID find a use for it on the very last boss... ;P Simply because it wouldn't steal the kills.)
The nature form was rather underused throughout the game. Granted it was VERY useful for scaling walls out of the water, it seemed its only true use was the Lobster boss and the blue plants. Every other form had quite a bit of use associated with it, but the nature form was basically switch to it and then switch back right away... It kinda bothered me... Though not too bad considering how often I used it as the beast form was the very last form I got. (Besides the obvious dual-form.)
Though even with those gripes, Aquaria currently takes the spot of the best game I've played all year.