Are there any substantial changes in Ocarina of Time 3D?

It will probably be 95% the exact same game if you take away the Master Quest. There might be a small difference here and there but overall don't expect to be playing a totally new game if you played Ocarina of Time back on the N64. That being said, the graphics are much better on the 3DS (not to mention, they will be in 3D). Expect to use the circle pad to move Link around, and then the A and B button, and likely a third button which will be "Z" from the N64 controller. More information on controls will be avaliable with the game in the form of the instructions.