So far the only games to make a FAITHFUL and consistently entertaining transfer from 2d to 3d have been.
Metroid, play super Metroid the Metroid Prime and see how faithfully the 3d game replicates the feel of the 2d one.
Zelda, Ocarina of time still one of the greatest games ever, need I say much more.
Mario, although we havent seen much though. The classic platformer sections in Sunshine made me feel a lot better about this trasition.
Prince of Persia has yet to prove consistent. And to be honest I dont feel any elements from the 2D game in the 3D game, and really thats what its all about.
Bad transitions.
Sonic.
Kirby.