I may try and recreate the game crashing on opening the menu in the first few areas and upload the logcat, since that might turn off a few people playing.
@False.Genesis: do you still need a save file to play with to try and get stuff working?
And as a final note, there's an app out there called
Sixaxis Controller that lets you use a PS3 controller as a native gamepad (or bind specific keys to buttons, depending on the game). Works great with Aquaria, just note that the help text still mentions Xbox controller buttons, so adjust accordingly. I can't remember the price off-hand, it isn't more than a few bucks. Note that you have to be rooted to use it because of how it handles controller connections.