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Without a doubt it was gen 3, because everything they did at that time was innovation. SMB - the "platformer". LoZ - open world sandbox adventure. Metroid, Kid Icarus - every new game was a new concept in theme and gameplay. They even through in hardware stuff like the zapper, powerpad, etc. Their 3rd party licencing was a major business innovation too. And as was said, the D-pad was a huge step forward in durability over joysticks.

SNES - brought some innovation in sound and graphics, particularily 3D animaton used in DKC.
N64 - true 3D graphics, rumble, and analogue sticks.
Wii - motion control, Mii's and virtual console.
WiiU - Touchscreen cotroller with speakers and mic, and MiiVerse.