Thinking back a ways, HTC at one point said he would like to add submarines to the game. The current water we have might make this kind of tough. Also, the shore lines always look so square and the water depth is impossible to tell.
I was flying over the thin cloud layer the other night right where the mountains come up through it. As I looked down, I thought how nicely the clouds wrapped around the hills and the way the terrain looked under the clouds.
Now, I thought further that this cloud layer could be set to 0 feet altitude and be given a differnet alpha setting and color and it would make for a pretty good water effect. If the terrain were rewoked to allow for negative altitude, oceans, lakes and rivers could all be made. The "water" could be made to fully cover the entire map and any terrain below 0 altitude would allow the "water" to show.
Further, If HT can give the PT a flight model, I would think it would be very much in their abilities to make a submarine with a flight model that would allow it to maneuver around in the water. Running into the terrain could result in a crash or a stop depending on speed.
Anti-sub aircraft could then be able to see down into the water and shoot at or drop depth charges on the subs.