Well, with flying in the game now we have three dimensional movement, so the system is already in place. They would just need to tweak it a bit to work in water, and of course design some killer underwater areas.
My only question is, would there be a limit to how long you could stay underwater? If so would it put stacks of "Can't Friggin' Breathe" on you until it killed you at 5? Or would it work like it did in FFX, where you can pretty much breathe underwater?