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I think it might be just better resolution. I don't think Twilight Princess Wii was different from Twilight Princess GameCube, other than 16:9 support and the map being flipped.

Also, have any of the 3D Zelda games ever been 60fps?
I know Ocarina of Time on the N64 was 20fps, and the 3DS version upgraded it to 30 fps, and the same, I'm assuming goes for Majora's Mask.
Wind Waker HD is 1080p & 30fps.
I don't know about Twilight Princess and Skyward Sword though.