Even then, that's not really innovation. The 3D is purely a gimmick, and considering 3D tech as a whole failed to find a place in the market and has almost completely died out except for movie theaters, I find it hard to say that Nintendo made the right call grasping at what was already unpopular tech. Ultimately, their use of 3D has done nothing to truly alter the gaming experience and can be classified as fun to look at but otherwise useless. Hell, I owned a 3DS, sold it, and when I got a new system, I went with a 2DS because I just couldn't be bothered using 3D and couldn't justify spending extra money on a feature that is so unnecessary.
Sony and Microsoft both have made leaps and bounds towards making the home console experience what it is today. Microsoft became an example of how good an online service could be on a home console, while Sony has established that they know how to handle a digital marketplace geared towards console gamers, integrating their various platforms across a unified account system and offering options like cross buy content. They both established the necessity for online services and social features as part of a dedicated gaming console, Microsoft probably more so seeing as they had created their Xbox Live service back with the original Xbox, no matter how poorly the system ultimately sold. Hell, Sony was one of the companies (besides Sega with the Dreamcast) that recognized the importance of disc based media and it lead to a huge shift in preference for basically all the third party developers (among other hardware differences between the N64 and PS1).
As far as home consoles go, Nintendo hasn't been innovating since the days of the SNES. After the failure that was the Gamecube, proving that it isn't just power that makes the console, Nintendo basically regressed and turned to gimmicks to maintain their foothold, ignoring common trends and features in the home console market, preferring their little bubble that only further isolated them from where the majority of gamers were shifting.
I respect that they've managed to hold onto the handheld market, although I wouldn't be surprised if the 3DS ends up being their worst selling handheld to date with further declining sales in successive generations.
As for PC gaming, I don't know enough about the progression of PC gaming well enough, and it becomes semantics arguing over whether PC or a home console did it first.