Well, you're comparing some of the earliest 3D games, on a console known for its crappy 3D, with some of the best 2D games ever made, on the last generation of 2D hardware. A fairer comparison would be VCS games to Saturn games, or Genesis/SNES games to PS2 games, since those consoles are at roughly the same points on the 2D and 3D timelines.

That being said, I totally agree that well-done 2D artwork has a timeless quality to it.

-- Z.