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That's a very, very tough call.
- SMB introduced 2D sidescrolling, which is still used to this day as the gold standard for indie game design.
- SM64 reintroduced the analog stick and non-tank 3D controls, integral to todays gaming.
- Love it or hate it, Ocarina of Time introduced (or made popular) contextual controls.

Considering I can't imagine modern gaming without any of these things, I can't give an answer.