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If we're ignoring the virtual console here, then N64 wins.

The Wii U overall had more great games. But for me Ocarina of Time, Super Mario 64, Banjo Kazooie, DK64, Starfox 64, and Mario Party are worth the entire Wii U lineup. The Wii U has more games that I really like, but the N64 has games I truly love.