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I think both are overrated by people wearing their chosen set of nostalgia goggles, but for me the N64 wins this pretty easily. There are two key reasons.

1. It was a genuine massive step forward for Nintendo, bringing their IPs into the world of 3D.
2. Ocarina of Time, whose importance and excellence can not be overstated.

I like the Gamecube, but I'd have to call it the weakest Nintendo home console. There just are less games that I love on that console than on any other Nintendo console.