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It’s really difficult to compare them.

GameCube wins in terms of:
3rd party support

N64 wins in terms of:
Mario & Zelda (IMO)
Cutting edge graphics

Wii U wins in terms of:
Multimedia device
Virtual Console

For me personally, I care more about gaming’s leap into 3D and the brilliant way in which some titles succeeded in doing it. So even though the library is balanced on GameCube, and Wii U had way better versatility, The Good Old Ultra 64 is my pick for best console in the category of least appreciated. It had some killer apps for its time.