In terms of FPSes vs. 3D platformers, I agree that the core FPS formula remains unchanged (but I mean, it's a genre, just like puzzle games or fighting games, so the genre tropes will always be there). However, if you look at Super Mario 64 in 1996, the big FPS that came out in 1996 was Quake. Compare Quake to the FPSes today and it's like night and day. Yes, you're still walking around shooting people in 3D levels, but you have co-op online and offline, massive numbers of people fighting together at the same time (64, 256, etc.), a boatload of stat tracking, RPG-style character outfitting and experience-point leveling, downloadable levels, the ability to record movies of your gameplay and send them to others, the ability to create and trade levels (a big deal in console shooters), and some stories that are actually decent. The featureset in today's top-tier first-person shooters has increased by several orders of magnitude. This is mainly out of necessity, since FPSes have flooded the market so developers needed something to set their games apart, but that's the way it's unfolded.
When you compare Super Mario 64 to Super Mario Galaxy, the featureset hasn't expanded that much. Not that it has to - Galaxy is undoubtedly an amazing achievement - but when I speak of my initial "meh" reaction to the game this is a primary reason. It's certainly a very innovative game, but I feel like it's innovative within the boundaries of the 1996 formula. It doesn't expand that formula into other areas like co-op (the ability to have one person use the Wii Remote isn't true co-op in my opinion, and is more of a neat bonus), or any sort of online play. That's what I mean when I say that I feel like I've seen Super Mario Galaxy before. It's because there isn't anything in the game that I feel is 100% new or groundbreaking; it's just the old formula executed to absolute perfection. And that's awesome, but I think it'll be appreciated more by gamers that haven't played Super Mario 64 or Super Mario Sunshine, so that newness is still there.