I used the 3D somewhat, but I lean toward leaving it off because it looks funny. That is of little importance though. I've played OoT3D four times so far. I liked
OoT 64 (and still do), but this was vastly improved. The graphics are breathtaking. Did you notice grass and flowers growing all over the place? The homes in Kakariko and Castle Town have more detail.
For instance, do you remember the lady in Castle Town who loves her dog, Richard? If you go to her house, you can see some fun things. Next to the lady's bed is a smaller bed, obviously for her dog. There are little dishes for the dog's food on the floor and on one wall are several pictures of Richard. One of the pictures is of the lady when she was younger and she's holding her dog. The houses in the original version were not nearly so interesting.
Another thing that I really liked was to take OoT3D with me wherever I went. As much as I like the console games and the larger screens to play them on, the one definite advantage of handhelds is being able to conveniently carry it away from home.
Did you know about the Skyward Sword pictures that are hidden in the game?