The 3DS game is the Definitve Version of the game, with upgraded Surround Sound & so fort.
Definitely play Ocarina of Time 3D with the 3D ON and all the way up, plus Surround Sound Headphones on. ULTIMATE ZELDA OCARINA OF TIME EXPERIENCE, 100% GUARANTEED.
I recommend something like "Plantronics Gamecom 777" for your Surround Sound needs on the 3DS.
EDIT:
Both the 3D & Surround Sound will blow your mind in this game.