I had both, I say the wiiu version has brighter colors and messages in a bottle are fun. I'd go for wiiu for the extras.

Definitely the Wii U for the sharp graphics.

you can also mod the gamecube version with betterwindwaker so that it has a bunch of the wii u features, including widescreen.

If you dont mind the artstyle change, go wii u, there are various fixes and improvements here and there that makes it more enjoyable, map on gamepad amazing too!