When it comes to innovation in RTS games, it's really hard to beat Kung Fu Chess ! http://www.youtube.com/watch?v=azzsuss-swo (Princes of Babylon - Meaningless Conversation)

It's chess without turns. Yes, you can actually dodge other pieces if you click in time and your piece is not currently on a cooldown.

The idea is both innovative and very simple. How come no one thought of this earlier ? The idea is also very elegant, if you can look past chess rules quirks like en passant and castling.