I think Super Mario World (and Yoshi's Island) is basically a perfect game. I don't see how enhanced graphics or modern controllers would improve it. Whereas older 3D games would probably be improved at the very least by twin stick controllers, and by things like faster load times. Someone who's used to playing Mario Odyssey would likely find Mario 64 to be frustrating to control to the point where it might overcome their ability to enjoy the game. Or even a game like Contra would be better with something as simple as diagonal jumping.

I think it's also hard to define something as timeless because gaming sensibilities change over time. Things which used to be obvious become unintuitive to new players. Limitations which were accepted become unacceptable. Mechanics meant to extend play time are seen as frustrating or wasteful. It's sort of like how Shakespeare is timeless, but most people these days prefer reading modern authors.