I'd say I prefer the 64/GC style, I truly love Mario 64 and I had a lot of fun with Sunshine even though it had a couple of obvious flaws. The Galaxy games, while there's not much I could criticize for what they were, never really made me love them.
I might have nostalgia bias for games with more open level design - I guess I'll know more after playing Yooka Laylee and Mario Odyssey.

I go more on a game by game basis I guess.. Cause I loved Mario 64, but really lukewarm about Sunshine (pun intended). I also wasn't crazy about Galaxy, though I did like Galaxy 2. 3D World was ok, but nothing special. 

Overall I prefer the oldschool 2D Mario games over all of the 3D games, though Odyssey looks like it took challenge that notion for me. 

Super Wario 64, Super Wario Sunshine, SW Galaxy 1/2 are great but they're not as good as real Mario games.

I haven't played 64 or Sunshine. Sooo I'll go with the level based.