Showing off the features of the 3DS version of The Legend of Zelda: Ocarina of Time at GDC, Associate Public Relations Manager David Young revealed that the upcoming game will include a version of the Master Quest. Originally available for the GameCube as part of a preorder premium for Wind Waker, the Master Quest was a reworked version of Ocarina of Time, mainly with changes to dungeons and temples to try and keep the game fresh for players who had already finished the original game.
I wouldn't go so far as to say this means you get two games for the price of one, but it's definitely a nice bonus for folks who have played through OOT a time or two, or who didn't manage to get their hands that Gamecube disc way back when. I'm pretty sure most 3DS owners were going to grab this just for bringing the franchise into another dimension, now they just have another reason to justify buying this game again.
Ocarina of Time 3D to Include Master Quest [Nintendo World Report]