Some Nintendo Innovations, since the SNES
N64 - controller, z button as well as control stick. Rumble pack
Gamecube - Mini discs, power packed in a small, quiet package, dual stick controller, arguably one of the most comfortable of all time.
Wii - Motion controls (many say that it is the ONLY way to play shooters, as since the introduction of the motionplus, it mimicks the sensitivity and twitch reflex of a mouse). Also virtual console, something that had never been done before; innovation through retro gaming? Oh, and Miis, which caused the other console makers to create avatars as well, they also started using miis in games, new concept-ish.
Wii U - Gamepad, one of the most under-rated (and underused) features of all time, plenty of innovation here, off-screen play being a huge one, and then basically every other feature in a controller all rolled into one controller. They also created mii-verse this generation, one of the greatest social gaming creations of all time.
I'm sure I missed many, many things, but Nintendo is the industry leader in all innovation, and this list is only their television based consoles, not their handhelds, where they have innovated a ton as well. Not to mention the amazing games that they pump out year after year.