I love Aquaria's metroid style, with the focus on searching the waters alone. But I think Aquaria could do wonders for more gametypes then that.
My idea for a mod would be a little more focus on rpg elements, mainly NPC's and more treasure that was more then decorative. My thoughts were based on the idea of Aquaria before the races became extinct... imagine all the dungeons in Aquaria back when they were populated cities, with the Kelp Forest being filled with Dryads and the abandoned city filled with Aquarians (or whatever the mermaid-like race was called).
This would be similar to the Aquarian Adventure idea, with an emphasis on puzzles and exploration, and possibly a decrease in combat. However, this would take a lot longer and much more effort.
Right now its only a very basic concept, but I thought I'd get it out there to see if it got anyone else thinking along similar lines. I'm thinking less rpg, and more along the lines of Zelda, personally.