It has been said that very few things in the Legend of Zelda: Ocarina of Time 3DS remake will be changed from the original. Nintendo confirmed that the pre-rendered backgrounds are all being replaced and the art style has obviously changed, but they've also said that there is no bonus content and it will be a straight port of the original.
However, Nintendo has recently also confirmed that the Ocarina of Time Master Quest expansion will be included in the OoT 3DS remake. Master Quest was originally released for the failed Nintendo 64 disk drive console expansion, which released in Japan only. But those outside the land of the rising sun, didn't get to experience Master Quest until the 2003 pre-order bonus for Wind Waker. That pre-order bonus was two straight ports (most likely emulations) shoved on a Gamecube disc as a free gift to those who pre-ordered The Legend of Zelda: Wind Waker.
The Legend of Zelda: Ocarina of Time - Master Quest is the exact storyline of Ocarina of Time, with all of the game dungeon's replaced with harder challenges and more difficult obstacles. So, if you weren't a Zelda fan back in '03 and didn't get the chance to experience Master Quest, the OoT 3DS remake will a great time to do it.
The Legend of Zelda: Ocarina of Time 3DS remake is expected to launch sometime around June with an expected MSRP of $40. Though it is possible that Nintendo could release this game as a budget title since essentially these games are straight port from 90's Nintendo 64 games. (fingers crossed for a $20 price tag)