When I hear underwater and Final Fantasy, I think of:

Beyond the deep blue sea

Underwater Ruins

And of course DONT TEASE THE OCTOPUS, KIDS!

Ultros

Octomammoth

Granted they arent underwater at all times, and we wont be in a XIV underwater dungeon, but you cant have an underwater dungeon without some sort of aquatic boss. Not to mention i'd love to see an Ultros cameo boss appearance since he works like a Gilgamesh style character.