I think rather than making it actually take place beneath the surface, it'd be a far better idea to simulate that it's underwater. You know, by making the ground look like sea floor, turning the fog up high, reducing gravity and increasing friction, and so on.
I'd actually love a low-grav' infantry map with sea troopers instead of regular stormies and Mon Calamarians instead of Rebels, and submarines instead of air units. Why? I just got a big-time X-Com: Terror From the Deep flashback
. Hiding in old wrecks, crawling through seaweeds towards an enemy encampment, taking cover behind big boulders, firing blasters and torpedoes at one another... it'd be awesome.
I'd love an X-Com-like map where an Imperial sub with sea troopers has been sunk and the Mon Calamarians send a sub of their own that lands near it and dispatches troops that are to neutralize the survivors and capture the wreck.

"One of the bitches actually gave birth while she was attacking, and her puppies joined in on the carnage."
--the awesomeness that is Boatmurdered.