3DS version is not that different from the original OoT, but it's easier to equip some gear, thanks to the bottom screen

nostalgiafags will say the N64 version is better. The 3DS version isn't that much different. Better graphics, most game breaking glitches fixed (misc glitches were purposefully left in for nostalgia factor), Master Quest mode (was originally gonna be a N64DD add-on but that thing flopped and wasn't released outside japan, MQ mode was added to a gamecube port tho).

Great game.

i prefer n64 version because I'm used to the controller

And that's the nostalgia bit.

Yes the controls are a bit awkward but they did make it possible to map iron boots to a button instead of going into the menu 50 billion times in the water temple.