One thing to admire about FPS games is the sound design; you can get important information about your opponent's whereabouts and actions by listening carefully to all the ambient sound. It's hard to implement something like that in an RTS because there is too much going on to have a lot of global sound effects, so environmental sound and the like have to be local - but you can only have them in places you already have vision of, so it's pointless. Maybe for an RTS that's different from SC2 it could work well, but I'm not sure.
I thought a potentially interesting way to replicate this would be that units can leave some sort of trail behind - like footprints or tire marks. A basic implementation might have all ground units leave subtle, but specific tracks behind that will last for around five minutes. If you have vision of these tracks you can follow them or you can just infer army positioning based on guessing, so situations might arise that require a talent for analysis. (think Aragorn in LotR ^^ )
The downside is obviously that it might interfere with visual clarity and also that it could make keeping track of enemy army movement trivial, but I don't think the latter needs to happen as it can be somewhat prevented by things like backtracking; so a good player can quite literally cover his tracks. - And the game can be designed around this anyway.
I don't know if a concept like this would fit Starcraft 2 very well, but in any case, it's more of a hypothetical idea for a new RTS and it seems 'obvious enough' (as in, someone probably thought of it before) that I'm curious if it was ever implemented in any other RTS game and if it was successful.