I'd argue that the Gamepad was a brilliant idea if it hadn't fallen flat on it's ass. The last idea that strikes me is the Wii motion control and Wii Sports. It was an instant hook for anyone I think. I think the 3D part of the 3DS is one of the stupidest things they have ever done I must say.
Currently Playing- Mercenary Kings- PS4, DBZ Budokai 3 HD- PS3, Forza 5- X1. Currently Awaiting- Destiny- PS4, Diablo 3- PS4, Forza Horizon 2- X1.
I'd say the analog stick. Sure they didn't really invent it, but they were the first to implement it in a mainstream system. And it's an innovation that has become the norm. You don't see controllers without analog sticks anymore do you? Motion controls were a fad and, thankfully, are fast fading. Dual screen is okay, but not nearly the innovation that the analog stick was/continues to be.