A bit late on updating this but the Master Quest version of the Ocarina of Time has been confirmed to be included into the Nintendo 3DS remake of our beloved OoT. The Master Quest was originally released as part of a Wind Waker promotion for the Game Cube but it is now being released as part of the highly anticipated Ocarina of Time 3ds remake.
The Master Quest features more puzzles, a higher difficulty, but still retains the story and framework that we all loved about the Ocarina of Time.