Me thinks someone watched Dr. Who last night
.
I was a fan of BioShock2,
And I think it adds a layer of underlying fear to the games environment. (Btw I think that's a good thing! And it worked really well in BioShock's case.)
(What if you get flushed-out or the base floods, drowning etc)
I think if it's done well, as with anything, it could be really cool.
I actually don't know much about DR. Who. Never watched. But, yeah, I agree about Bioshock. That aspect of being so deep in the ocean with the unknown. Even more so if it was on an unexplored alien planet. Beautiful but terrifying.
Hah, I was wondering when SOMA would start getting referenced around here
and I am saying this with no negative connotation whatsoever; everything should be taking more cues for SOMA, though I am saying that in my capacity as a semi-rabid Frictional fan 
Anyways, I would be all for aquatic environments/underwater missions. As above posters have mentioned, Leviathan was an interesting take on the whole "water" theme, would love to see more.
Yeah, I just finished SOMA and the facilities, robots, music, and other aspects really reminded me of Mass Effect.
I think an underwater type city of some aquatic race or a facility of some Corporation could be interesting if it fits and makes sense with the setting and story.
@Sojourner
That city is beautiful. Would definitely like to see somthing similar to it