Was the transition from 2D to 3D inevitable?

[Aulos]

Assuming that time, yes.
But I see a comeback to 2d in many new titles, and we can see something like that in the next generations.

Something like "link's awakening" for gen 9 for example.

Link's Awakening is still a 3D game, though, just in the "2.5D" style, much like Pokemon X/Y and OR/AS. GF released a 2.5D Pokemon game just last year - Lets Go Pikachu/Eevee. I really hope they keep that style away from mainlike Pokemon games. That time has passed.

With Zelda, there have always been 2D/2.5D games releasing on handheld platforms alongside the 3D console games. The Link's Awakening remake is just falling along those lines and is not indicative of any kind of new trend.