Sorry, but the Clone Wars were the biggest letdown in cinematic history. They should have just been left to myth, to the references Ben Kenobi makes that made them seem much bigger than they turned out to be. Why? Because there was never any suspense to them at all. Not only did we all know what would happen thanks to the fact that they took place in the prequel era, but there is no room in them for any of the "what if" scenarios that made Empire at War fun. What would have happened if the Separatists had won? The same exact thing. Palpatine would have come to power as Emperor, since, after all, he was running both sides of the war and ended it whenever he felt like.
Aside from that, the prequel era really does not lend itself to the RTS genre. The intrigue (if you can call it that) of that period is more suited to RPG games. A prequel-era RTS would be like saying, "hey, let's have WarCraft be set in the French Revolution!" We all know what happens on a grand scale in the prequel era. What we don't know, where there is room for storytelling, are individual characters' stories.