This is a very cool and well thought out idea- i can't wait for the release.
One thing that bugged me about underwater maps was that, there are no swimming 'animations'. In reality it's impossible to walk underwater unless you have a very heavy suit on, so i hope when you say 'water pressure on units' , you mean that the units will walk slower and be "weighted down". Follow me?
A few more questions/comments:
great models!
For the Scuba troopers, My thoughts are to have them carry blaster rifles, harpoons, and rocket launchers. (each a different unit) Also, For the blaster rifles, you could make them more "beam like" and maybe be a bit "squiggley" (is that a word?)
And then, it'd be great if you could make a model of the Quarren underwater vehicle!