I enjoyed almost all of the improvements made to the 3D Remake.
The first thing to mention are the enhanced graphics. They are simply gorgeous. The character models look superb, the textures are nice and detailed, and the particle effects look better than ever. Very good.
The increased framerate also improved the experience for me. Everything felt much more fluid than before. This was gilded by the better animations that the game provided. Everything feels much more natural and less stiff when compared to the original game.
The touchscreen functionality for menu navigation was a welcome addition for me. Navigation and selection was very quick compared to before. Also, the inclusion of an additionl slot to equip an item made everything that much more convenient. Even more, changing the boots from equipment to items was a smart move. Switching to the Iron Boots was no longer tedious as it can be done in real time.
I didn't really care that much for the gyroscop use. I feel more comfortable holding my 3DS in place rather than moving it around. I leave the feature off whenever I play.
Now we come to the Masterquest. This was a big selling point to me, as I have never played the original Masterquest before. The inclusion of the mirrored world and stronger enemies made it even more appealing. When I played it for the first time, it felt like a completely different game. The challenge is there, and the dungeons had interesting twists.
Now, the only things I didn't like were the absense of glitches and some content that was altered in later versions of Ocarina of Time. Of course, this is a very minor complaint, and can be remedied by popping in my original cart into the N64.