Well they added the Master Quest version of the game as a bonus. But they took out the Stone of Agony, because the rumble feature isn't available and put in a replacement item that is supposed to do the same idea. As far as I could tell the dungeon layouts and everything are the same and the quests, etc are the same which I like. Basically the 3DS version, as far as I can tell, is just a graphically overhauled update of the original. Of course, that's what I like about it, because they didn't dick around with the layouts/gameplay. Of course, they did make it so you can aim your slingshot/bow/hookshot and 1st Person view by moving the 3DS around (but I still just normal aim, cause I'm not a fan of gyro controls).
As for the 3D, it is very well done. I can play that game in 3D for hours on end and rarely switch it off.