I think it's pretty flawed to look at innovation solely from a control standpoint.
Microsoft: Has made huge strides in the online functionality of consoles, had the first built in HDD, unleashed achievements upon us all.
Sony: DUAL MOTHER #### ANALOGUE STICKS(way bigger than motion IMO), rumble/motion feedback, a (failed) attempt at Motion/voice control with the EyeToy, cemented the notion of consoles as a multimedia device and not just a gaming machine. Then there's also CDs. They may not have been the first to use them, but they were the first truly successful console.
Which brings me to another point - nearly every idea has been done before and innovation alone is never enough. The fact that the Dreamcast was the first system to have built-in online play or DLC didn't save it. Motion control is really old, Wii is just the first successful use of it.
Nintendo likes to play it safe at times too, by the way. Just in different areas. Did I mention CDs? Or their absolutely terrible online support for the past decade? Or maybe how they have depended on the same tired franchises for decades now. Their third party support is truly horrid compared to Sony/Microsoft.
Sony/Microsoft may not be completely revolutionizing the input method for games, but they fine tune many other areas that I frankly couldn't live without. Areas that Nintendo is trying to play catch up on, just like how Sony/Microsoft is play catch up on these new inputs.