The 3D genre in general was more diverse in the N64/PS1 days, IMO. Right next to Mario 64 you had stuff like Hybrid Heaven, Winback: Covert Operations, Castlevania 64/Legacy of Darkness, Mission Impossible 64, Diddy Kong Racing, and Bomberman 64 just to name a few off the top of my head. Many of those were way ahead of their time, or unique even by today's standards.
But anyway, Glover, Bomberman Hero, and the Chameleon Twist games should be noted from the old days as experimental 3D platformers with a lot of charm, even if rough around the edges.
These days, I've heard and seen some images/videos of various projects that former Banjo Kazooie developers have been working on. Some of it looks promising, but none of it has made it to a major console that I know of.
Shin'en released "Jett Rocket" for WiiWare in 2010. I played a demo. It has the basics of the N64 3D Platformer days in it. Something seemed to be missing, but it might be one of the closer things in recent years. Oh, and the new Pac-Man Ghostly Adventure games (2013 and 2014) look like they have a ton of great ideas in this genre, but also seem too unpolished to be consistently enjoyable.
Fun fact...I only just last year beat DK64 with [Edit: 101%] completion. I have to say, after walking away from it for years, and also not having a lot of games like it come out, it really is a fantastic game. Some games from those days basically gave you more to do than you could accomplish. I also recently unlocked and completed the bonus world in Bomberman Hero (not easy to do), only to find out beating that unlocked a new side-quest and an entirely remixed quest from the beginning of the game! And Banjo Tooie...I still haven't beaten that one. Something was off about that entry in its spirit, beyond the crazy amount of collectables. It felt almost self-destructive in terms of its story and environments.
The Mario Galaxy games are amazing, but their format inherently has a little less focus than Mario 64 or Banjo Kazooie in level design, which makes them seem a little less substantial in some terms.
Anyway, I'd love to see some more 3D platformers.