ocarina of time 3D was better in my opinion because it had much better graphics. but thats not the only reason though, i dont like judging games only on graphics.
its better because, well... you could take the adventure with you. because i own a lot of console games that i really love, but can only play when im home. but because OoT is on the 3DS now, i dont have to worry about one of those games anymore! (now all i need it super mario galaxy, majoras mask, and kirby on the 3DS...)
another thing was is that i love all the patterns that games have on certain things inside them. like, i love colorful games that have a lot of design in them. and the original OoT on the 64 had very dull colors. the 3DS one though, its like theres color everywhere, and i love it!