Definitely depends on the series.
I think I have come to appreciate 3D Mario more than 2D Mario as Odyssey is way more appealing to me than the NSMB series.
Although I am really into Metroid Prime, overall I have to give the 2D Metroid games the edge. Zero Mission, Fusion, Samus Returns, and Super just can't be topped.
Zelda I am a little conflicted about. If you asked me before BOTW, I would have said 2D because of my love for ALBW and Minish Cap and Adventure of Link (and so on) compared to my relative apathy regarding Twilight Princess, Ocarina of Time, and Skyward Sword. In a post-BOTW world though I can see 3D Zelda being the preferred format for me.
What I can say for sure is that the half measures between 2D and 3D design for each series (3D Land for Mario, Phantom Hourglass/Spirit Tracks for Zelda, and Other M for Metroid) are not good. Don't try to blend again because it's a disaster.