I kind of prefer Ocarina of Time 3D. Sure, the original looked great and played great for its time and was very revolutionary, but the 3DS version of the game is just... better, in my opinion.
The 3DS version looks nicer (mainly referring to the graphics) and the character models are improved. The one thing about the graphics I love most is the sky, though. The sky, no matter what time of day it is, is exceptionally beautiful. I know it's not important in the grand scheme of things, but I just really love the views of the sky in the 3DS version.
The controls are much smoother in the 3DS version, too. The touch screen menus for the items and equipment was very efficient, and changing the Iron Boots and Hover Boots into equippable items almost entirely removed tedium. Not to mention the Ocarina getting its own button, and a fourth slot for items being added, really made the item system much smoother and practical. The gyroscope controls were very nice too, particularly when it comes to aiming with the Bow or Slingshot. It feels very natural to aim with the gyroscope, and it's also very easy to use.
One thing I'm a bit unhappy about with the 3DS version, though, is that it was dumbed down a bit compared to the original, in regards to hints and clues. Specifically, when confronting Mido on your way to the Forest Temple, he says that "if you really were Saria's friend, you'd have some kind of proof" or something along those lines, hinting for you to play Saria's Song for him. If I recall correctly, Mido never said that in the original. Hints like that were added, and while it isn't anything major, it still bugged me a bit.
All in all, I think the 3DS version of Ocarina of Time was a major improvement over the original. Of course, this doesn't make the original any less amazing.