2d gaming has a level of polish and refinement that has NEVER existed in 3d games regardless of the genre.
There are plenty of 3d games with polish that surpass their 2d equivalent/predecessor, like OOT vs LTTP or FF7 Vs FF6. But it's a matter of opinion I guess.
In some cases it's a regression and doesn't work as well, like sonic going 3d.
In terms of platformers, super mario 64 is as polished as they come. I wouldn't rank any of the 2d mario games above it, but again that's a matter of opinion.
There are many 3d game genres that simply wouldn't work in 2d, they are like two separate branches of evolution in gaming and can't really be compared like for like as the presentation is vastly different. It's like comparing a canvas to a sculpture, both are art but you can't say one is by nature better. That's what I think anyway.
I have to give props to the original Tomb Raider though. It used to get a lot of flack for "tank controls" and slow gameplay but man it was one of the most precise 3d platformers ever made. There was essentially two types of jumps. A short jump, which just required you to get to the edge of the ledge you were standing on and simply jump forward, and the long jump, which required you to get to the edge, hop backwards, then run forward and hit the jump button. One of the earliest examples of platforming in 3d and the game nailed it.
Tank controls made for enjoyable precise platforming, yes. But more like a puzzle platformer, slow and methodical. Mario 64 is fluid 3d platforming, precise, tight controls, huge move set (for the time) and wonderful playgrounds to show off just how good you were at controlling mario. It requires quick reflexes and had the same fluidity as the 2d games.
It's not platform games. Mark of the Ninja > any 3d stealth game.
Tenchu 1 wipes the floor with it,
just my opinion fact. Also mgs, literally any of them?
I found mark of the ninja to be so linear and it's presentation felt almost like an evolved flash game. I tried so hard to like it.... Within the Blade is much better for me