I'm not colorblind, and I'm doing fine in the game; however, I've met two friends today and tried to convince them to try Aquaria, only to run into trouble during the demo because they're colorblind, and can't open the flowers/do other puzzles when they're just color-based.
As far as I can remember, there aren't THAT many things in the game that are solely based on color, but might it be helpful to provide a colorblind mode in which, say, the flowers would show the appropriate symbol needed to open them instead of just color? (also those fish that swim towards the color would need to have the symbol on them)
I realize in each of those situations you could just cycle the color wheel until something happens, but I imagine that must be frustrating to colorblind people.
Heck, if anyone's interested, it could be something simple enough to integrate as a mod.