Ooh, I can think of several 2D games that would be cool to see in 3D, but it's harder the other way around, I think.
Adventure of Link would be good, like
@MW7 said. A huge open world like BotW, but with actual dungeons (!!!). I could see that.
Link's Awakening would be interesting, too, mainly because you'd have Mount Tamaranch visible from pretty much anywhere. It'd give the game a strong sense of place, with the Wind Fish Egg being like the Moon in Majora's Mask, a constant presence.
Aaaahhhh, I'm torn between Oracle of Ages and Minish Cap.
Minish Cap's shrinking would be a lot more impactful in 3D. The size differences could be really emphasised and played with, and the level design could incorporate more verticality, which the shrinking lends itself to but 2D struggles to deliver.
But Oracle of Ages in 3D would have Link in a mermaid tail. . .
Think of the fanart
As for a 3D game going 2D. . . Errrr, I dunno.
Majora's Mask might work because the world is more compact and everything being in cardinal directions would work with top-down movement, but you'd lose the Moon and the world would probably feel less 'real', which is where the game gets a lot of its strength.
Ocarina of Time would probably be the easiest to translate to 2D. I don't think Twilight Princess is as suited to it because the wolf transformations might feel weird and the grand scale of the visuals would be lost. Ocarina doesn't have those issues. I dunno. I suppose I think Ocarina has the least to lose.