Not sure if this would actually be considered an RTS or some other type of game, but does anyone remember the old Myth games? They were basically like fantasy battle simulators, where you commanded a given army of troops. The battle controls were superior to something like Warcraft or Starcraft, but the focus was on specific mission-like battles, rather than base and army building and resource gathering. You didn't control the army in between battles. You basically used what you were given as best you could. What I liked about them was that they took place in real time at a pace that felt like real time while you did things that made sense in real time.
In a game like Age of Empires or Starcraft the action unfolds in real time but it is kind of a weird, distorted, abstract flow of time. For example, in a Starcraft battle seconds can matter as you move and coordinate your forces. It happens at a pace that feels like a real battle. But while your troops are fighting you can be training new ones back in your base, building new tanks, and assembling new star cruisers in time to send them as reinforcements to the battle. I love Starcraft, don't get me wrong! I think it is a wonderful game, the likes of which we may not see again for some time. But I've always found that odd time disconnect weird.