My all time favorite RTS is Company of Heroes. What made it stand out was the way the game forced you into constantly fighting and trying to fight attack your enemy. It also had squads which is a feature I really really like because it reduces the number of command units you have to deal with. It also incorporate cover really well. It also had things like suppression, pinning, and retreating which really upped the tactical decision making of the game. Most RTS games are rather bland with their combat IMO, but the way they did it in Company of Heroes was great.
I agree, imo CoH is hands down the best RTS out there and by far, They introduced a tactical approach to combat that you can find in more hardcore tactical RTS's like Close Combat series where you have pinning, arc of fire and all that good tactical stuff, a little simplified to fit mainstream standards of accesability but not lossing it's realistic feel.
And that leads me to an idea that introducing realistic game mechanics into the RTS genre will add depth that will make it stand out of the crowd.