The Gentleman said:
I do think Hydrophobia was certainly a step in the right direction, but there's two big obstacles for such levels.
1) The kinds of things that would be on equal footing with the player would be floundering as much as them.
2) The kinds of things that would be native to the water would likely way outmaneuver the player easily.
In other words, underwater combat gets stuck between two extremes: either your opponents are easy pickings or you are...
What about a game where you played as a sea animal, or at least someone much more at home in marine environments (I'm imagining something like a Zorah from Zelda) or using technology that would grant improved human maneuverability (some kind of fancy scuba suit with jet propulsion or something and a fancy harpoon of some kind.
Or to go the opposite way, survival horror game. You were a passenger on a ship and it sunk and got invaded by crazy deep sea monsters. The ship is slowly filling with water so you only have a limited time to get out before you run out of air. You have limited tools available that must be found around the ship, like flippers, goggles, flashlights, flares, glowsticks, and scuba gear and you have to navigate the infested ship hull to escape. If put in the right hands (Frictional games or the dev who made Outlast) I think that would be an extremely interesting, beautiful and deeply HORRIFYING experience. Use the fact that everything outclasses you as a reason why you need to avoid combat as much as possible, because chances are you'll lose.
Or you could create a game where you're a deep-sea explorer version of Thief. Raiding sunken ships for treasure while avoiding the dangerous predators who live there.