There was talk about the clouds about two-three weeks ago on a fireside chat. If I remember correctly, they chose these kind of clouds because of visuals - pre-rendered clouds would have looked more stale. I'm not sure if this is something that is feasible to have as a "switch" under options - I mean, choosing between cloud rendering types in a MP game where choosing one of the options practically gives you an edge. However, I'm not a programmer or a game designer by profession.
There are problems with the clouds as they are, though, as you mentioned. In addition to sometimes seeing enemies in/behind clouds in the middle of the match, sometimes you can spot enemies behind a cloud if it has not been rendered on your screen yet, and there's funky stuff going on with the captain's spot in that regard too.