Coming from Fez creator Phil Fish...

We don;t have any plans for that, no. people keep assuming fez would be a no-brainer on 3DS, but in truth it would be kind of pointless. the game is practically always shown in isometric 3D, there’s never any perspective there. i don’t think it would work.

While the wording seems a bit harsh, I can see where Fish is coming from. Adding in actual 3D would kind of take away from the way the game's visuals trick you. It would also impact the puzzle design in some elements.