On the whole, I prefer Ocarina of Time 3D. The text is faster, the animations are smooth and the visuals are crisp and wonderful.
However, it's not a perfect upgrade - there are still one or two things that I prefer about the original. I do believe that the newer version has been dumbed down slightly. I'm not just referring to the Sheikah Stones here, which after all were optional.
Here's one example. In the original version, during the Biggoron subquest you were often not actually told explicitly where to go in order to advance. For instance, when the Cucco Lady gave you Cojiro, she mentioned her brother, but did not say where he might be found. However, the game gave you a hint about his whereabouts - Cojiro gives a call whenever you enter the Lost Woods.
In Ocarina of Time 3D, however, that hint system is eliminated altogether. Cojiro no longer calls when you enter the Lost Woods, because the game simply outright tells you to "go to the location marked on your map." For me I suppose that's not such a problem, given that I know
OoT like the back of my own hand these days, but I do think that it would dampen the challenge and that wonderful sense of adventure a bit for a newcomer to the game.