I played Banjo Kazooie Nuts and Bolts about 4 years after its release... but that's kind of the opposite situation. I was one of those people who was very upset it wasn't a platformer, but wound up loving it.
I played Metroid Prime at least a few years after its release, and was blown away. I feel like it's probably the best example of transitioning from 2D to 3D and keeping the game's spirt in tact.
I'm a Marvel fanboy, so I was biased against Arkham Asylum by default. But I played it, and had to admit it was the best superhero game released to that point.