I think old 2D games still hold up very well, especially from the SNES and GBA gens. I mean, can anyone honestly say that Secret of Mama, Chrono Trigger, DKC, Megaman Zero and Drill Dozer have aged poorly? I'd also argue that Chrono Cross is as good or better than any other modern turn based JRPG.
3D games had to struggle with camera issues during the early days, which majorly hampers them in comparison to today's titles, but there are still certain design elements, and entire genres that have nearly disappeared today. The loss of the 3D platformer in modern times is a shame. What counts as platforming these days is basically just holding the left stick in the direction of a ledge to "jump." I feel like puzzle solving in action adventure games stopped being a real thing recently as well.
Also, Quake is still the reigning champion when it comes to fps's. I modern quake-like could probably surpass it, but fps design trends have gone in a totally different direction.
