IMO the graphics were a step backwards. Everything is so much brighter in the 3DS version, it just makes everything unrealistic. I haven't actually played the 3DS version, but I've seen videos. The Lost Woods just isn't the Lost Woods anymore. What happened to all that mysterious haze?
The 3D graphics in OoT3D are some of the best on the system and everything in the game is all polished up.
I like the master quest and all of the little changes like the happy mask shop owner's bag from MM and the Skyward Sword easter eggs.
To me the 3D version is exactly what the developers wanted for the game but obviously couldn't achieve at that time.