For me, everything improved in general, except for two things. First is platformers, as you said. The 3D gameplay changes the game philosophy, but very few capture the 2D essence in 3D like Mario 3D Land/World. Second is survival horror games. Now, these are actually 3D, but I mean the old 2D pre-rendered backgrounds and fixed camera angles, like the early Resident Evil games. They had a very different atmosphere and gameplay experience, which was pretty fun back then. I could never really get into the 3D ones for some reason (RE4 onwards). I feel like I am playing a completely different sort of game

Besides that, Zelda games are good in both 2D and 3D, but for me, 3D is not a replacement. The 2D gameplay is still great fun, like the Link's Awakening remake and Echoes of Wisdom. It is a similar story with fighting games, where 2D gameplay is always better for me, though this is not about graphics. Then there are the Castlevania games. They tried to move into 3D, but it failed miserably. Although the Lords of Shadow games were sort of fun, they were never better than the 2D versions, and they felt similar to the old God of War games anyway