There's the matter of how much games have been able to improve upon something that an earlier game did. There's no doubt that the more recent 3D Mario games have tighter controls, better camera, etc., but they're not fundamentally different when it comes down to it. Never mind the countless other games that have used and perhaps refined the formula in their own way over the years as well.
Mario 64 isn't even in my top 3 favorite platforming games, or even my top 3 favorite Mario platforming games, but it got so many things right nearly 3 decades ago when it didn't have the benefit of cribbing off of someone else's work and hasn't had anything since come along to redefine that genre in the same way it did that it's clearly deserving of being among the finalists.