The original naturally has a unique charm which even the remake can't touch.
However, since the remake is an enhanced version of the original, only made better, it is obviously the better version of the two.
OoT 3D is actually what the game was supposed to look like. And not the N64 version. Miyamoto (I believe) said there were two games severely held back by the N64 hardware and could not realize the original vision. These were OoT and Starfox 64. Both were remade. If you look at the original concept art for Zelda, you'd see that the 3DS version comes a lot closer to realising that look.







