Syp at Bio Break expresses his disdain for underwater environments.
I generally agree with him in regards to full underwater zones. I hated Vash'jir in Cataclysm. I think that 3D is generally not suited for MMO movement. Underwater also feels like it punishes melee more than ranged, as melee depends more on moving than a ranged caster who can stand still and nuke.
However, I like having water in a regular zone. Like a lake, and a quest sends you to find something in the lake. It changes the rules of the game, but in an intuitive manner. You expect to be slowed down, to have drowning mechanics. The experience is short enough that it's interesting, but not long enough to outstay its welcome.
Alternate environments where the world "rules" change significantly are fun in short doses. I would love to see an outer-space, zero-G mission in SWTOR, for example. But like any good idea, alternate environments can be taken too far.