There's been a recent boom in retro-style 3D platformers, so there's no shortage of good options to choose from:
Bomb Rush Cyberfunk
Lunistice
Pseudoregalia
Toree 3D and the rest of the Toree series
Frogun
Corn Kidz 64
Cavern of Dreams
Upcoming:
Toree Saturn
The Big Catch
DoubleShake (technically 2.5d)
There are more, but these are the ones I can think of.
I also struggled with getting my 8bitdo Ultimate controller to work on Linux. My solution ended being to use a Mayflash controller adapter to trick my PC into thinking it was just a normal Xinput controller, while the adapter itself thought it was a Switch Pro Controller. I've since become a huge fan of these little adapters, as they basically make any controller compatible with any platform, including Linux, so that's one less annoying compatibility issue to deal with.
If you have the PC for it (or a Steam Deck), get it on Steam. Not only will it look and run better, Steam Workshop is full of amazing community levels, costumes, and custom abilities.
Pepper Grinder is an amazing little retro-style 2D platformer that took the burrow ability from Ori 2 and made a whole game around it. It's novel, fast-paced, and surprisingly polished! Made me wish the demo was longer than 3 levels.