This is gonna be kind of a "WTF" to some people, but I thought Castlevania, Sonic, and Mega Man made the best jumps to 3D. Castlevania: LoI and the newer one (I forget its name) were pretty damn good 3D games. Mega Man Legends was a fun MM series, even though almost all classic Mega Man references were gone.

Sonic should really explain itself. SA1 and 2 were pretty good. Some complained that other characters were playable, but those same people are the ones who wanted more playable characters anyway.