I has been posted earlier that the whole point of cloud city being so "in the clouds" clean, pristine and nice was a metaphor for something that is nice on the outside but hides all the evil on the inside/lower levels (carbon freezong chamber, places where duel scenes take place). That being said, we could stick with the cloud city exteriors as they are, not with moody clouds. In ROTS the cloud formations strike a different metaphor: "everything around in the republic is turning dark" hence the dark skies near Jedi Temple, Senate and the like....it's just about different visual metaphors