You probably won't be able to change the main character too much. You might be able to replace the skeletal file, [effectively letting you make Naija look like anything, as long as you meet certain requirements] at some point, but I don't think its possible yet. The controls for the player are hard coded, so they won't be able to be changed that much.
The main menu and other hud elements won't be able to be replaced either, at least not in the first iteration.
The main focus will be to let you make new environments for Naija to explore using the Aquaria game play systems. You'll be able to script and animate new creatures, make up your own weird puzzles if you like, create an area with all your own images or use graphics from the game, use the included music + sounds or your own... etc.
It should be possible to create a whole side story adventure if you wanted to.
As more people fiddle with the tools, I'm sure we'll figure out what other weird things are possible, and I'll probably release some patches to make the editing process easier after we get feedback from people who have tried it out.
Someone pm-ed me about doing a full conversion of AQ to make a remake of
Exile. I don't think it'll be completely possible with the first release version, since you'd have to replace the character and add some extra functionality to the controls. But it might be doable in a later release.
Creating the level and enemies would be easily done from the get go, tho.