Oh boy, someone posts this every other month and it always ends up with the same answers.
Super Mario 64 was the first jump to 3D that was fully competent, I know looking back there's some heavy golden age thinking going on, but the only other game that I played and I was like "wow they get what 3D should be" is Ninja Gaiden 1.
Many game makers still don't understand what 3D should be, what it's devolved into now is pretty bland levels that are filled with filler everywhere to make them look lively when in reality you've just got some very basic polygons stitched together. For 85% of the 3D games, they've all taken a step in the wrong direction. Game development is going backwards. The best metroidvanias are still in 2D, because the ones that are in 3D are mostly fucking messes, Metroid Prime was pretty good, but there's still something missing from 3D Metroids.