A real time strategy game, set in the zelda universe could be ok in my opinion.
However, since nintendo never will give away the license to any other company the game would be played on the wii.
The wii is not directly famous for its good graphic.
Would you like to play a RTS with medicore graphic and has the same thing as any other RTS and the only diffrent that it is zelda?

I don't say the idea is bad (yes you did)but I would not buy a RTS for the Wii just becuse it is a game that has zelda in its title.
What would the game name be?

The legend of zelda:Ganons Invasion, that feels a bit cliché.

A RTS zelda could on the either side be very good or very bad or most likely in my opinion medicore.