You know, I don't play C&C for the same reasons I play, GG:WAW, GoA or even CotA. C&C is kinda like those "tower defense" games, where you build a bunch of defenses to try to stop an endless onslaught of enemies (a pretty common genre of java game these days). I play C&C for visceral action. I play the more "hardcore" wargames to be able to think things through, plan, check exact unit strengths, and so on.
I disagree that the CM:SF style game is going in the way Yoozername suggests. This might be an "option" for some of those games (along with LAN or PBEM) but I believe the core game will stay solo and WEGO, Turn-based, or Real-time with pause. The demographic just isn't there for detailed Real-Time multiplayer wargames. Look at Take Command, where you technically, within a multiplay setting, could do the things you are arguing (players could take control of various command levels, get orders from superiors, leading brigades, divisions, and whole armies. It was well recieved by the wargaming community and critics, but games last hours... many many hours even if solo, and I wouldn't say it was a financial success.
To use TOW as an example of an effective genre that will spawn an "innovative" mix between simulation and game is a bit off as well. TOW is lackluster at best, and its own development is plagued by setbacks and bugs. Think of incorporating a complex mutliplayer engine, as posited, within the already complex system of TOW.
I have no doubt that this method will be looked into by developers, and possibly used. But I think RH got some of it right. Most people are looking for a GAME not a simulation. In a situation where your fun factor relies upon other people online to cooperate with the company you lead, you find that this quickly breaks down when people lose hours to a "griefer" or just a bad player. In a learning situation, at a job (like being enrolled in the armed forces) you worry less about this stuff. In a game, which competes with other games and real life, not having a way to keep players on task or to properly match players would really throw a wrench into the game.
"Neca eos omnes. Deus suos agnoscet!"
(Kill them all. God will know his own.)
-- Arnaud-Armaury, the Albigensian Crusade