I've thought that an interesting mod would be one that makes something similar to the Boss Rush mode in Kirby Superstar or something - basically, what I envision is a line of caverns connected by tunnels, and it would be a pattern - You'd start out in a room with a save crystal, some recipes/ingredients/powerups, and such, and then you swim through a tunnel and there's the first boss. You beat it, and swim through a tunnel to another room, that has another save crystal, perhaps some healing items, and then you swim through a tunnel to the 2nd boss, and that pattern proceeds all the way to the end.
But then I've been told that because of how the Aquaria bosses are actually designed, that's not really possible or easy to do. Oh well.