Okay - I'm a little ignorant when it comes to copywrites, trademarks, etc, but isn't releasing the source code pretty much an invitation to do whatever you want with the game? IE, release it commercially or whatever? I assume it wouldn't be such a big deal if it wasn't significant in some way.
Also, it seems to me Aquaria 2 would take less work than Aquaria 1...couldn't you use a lot of the same mechanics, creatures, etc in the second game as well? Except maybe you could add a few more simple mechanics for the land and/or flight based portion of it(since he was last seen in a flying boat, it makes sense for the game to add more land element).
Considering how advanced the mods already are, I don't care really, I just want more Aquaria

I wish Alec hadn't burned out on it from the criticism. Aquaria is basically art, and you can't create art without expecting art critics to fling shit at it regardless of how good it is. Sure, it's not perfect, it's probably really freaking hard to perfect a game with such a small team of testers(since testers weed out the little stuff yes?), but the overall game is incredible.