I have played both Twilight Princess on Wii as well as GameCube on dolphin...
Though the game textures are same on both, I noticed a FPS decline on the Wii version while a full speed on GameCube version...
Why there is a difference in performance????
Dolphin disables Skip EFB Access to CPU automatically for the Wii version but not for the GameCube version. The Wii version requires it in order for aiming to work, but the GameCube version doesn't since it uses a different aiming system. (Both versions also require it for lens flares to render or something like that, but that doesn't really have any gameplay impact.)
Maybe there are other reasons as well, but that's the only one I'm well aware of.
GameCube version is in 4:3 while the Wii version is in 16:9. Seems to me that the GameCube version has less of an area to render at once (culling that which is out of the camera view). I don't know for sure how much impact it will have.