Honestly, I'm surprised that no one has attempted to make a major RTS for the Wii (is there even any at all, besides Pikmin). The Wiimote would work pretty good, better than an analog stick, for sure. The Wii is more than powerful enough, Starcraft ran great on PCs with less than 10% of the Wii's power. Heck, one of my favorite games was "Warlocked" which was a really, really fun RTS for the GAMEBOY COLOR. (Anyone remember that game?)
If someone can make a damn good RTS that runs on an ancient 8MHz Z80, with 2 buttons and a D-Pad, the Wii should be more than capable. But I suppose companies assume Wii owners are too stupid/casual to play an RTS...
Hmmm. Now I'm just imagining "Mariocraft". You choose either the Mushroom Kingdom or Bowser's forces, and build up Goombas, Toads, Koopa Troopas and Yoshis to fight the other side. That would be awsome.