Yeah, that could actually be pretty cool. I'vee yet to see an underwater MMO. 2D would be easier to pull off, since when MMOs are in 3D they're still bound by gravity (except for flying mounts), so it's easier to direct people to where they need to go for quests and such. Imagine using a 3D map. The Metroid Prime series uses them, but I find them really confusing. Still, could be done, and it would be an amazing experience being able to swim anywhere in a 3D environment.
Different races like the ones found in Aquaria could have special attributes and classes, too. I can't help but think it would be better if the battles were more action-oriented than just going up to an enemy and hacking away at it. Zooming at them to cling onto them or to take a bite out of them, maybe. Different races would also have different ranged weapons, like Naija's energy Form vc. her Beast Form shots, which could make for interesting battles.
Combining ingredients to make food would definitely work in an MMO,plus being able to make armour (sea urchin armour crafting, anyone?).
I dunno, you guys come up with something now.