A few years ago Nintendo said that they were considering a remake of Majora`s Mask for the 3DS. They were deciding between two Zelda games for the Nintendo 3DS, it was either Majora’s mask or it was going to be the sequel to Link to the Past. Nintendo chose to do Link Between Worlds. This was said by many to be the second best game.
The Nintedo team working on Zelda is big and they can work on two Zelda games at a time. Last year they worked on Wind Waker HD, Link Between Worlds and Zelda Wii U. This year a lot of attention has gone to Zelda Wii U, which is the biggest game that Nintendo has ever developed.
It could be that Majora’s Mask 3DS is being developed by Grezzo, this is the company that gave us Ocarina of Time 3DS. This would make a lot of sense as they know the core systems and they have not been working on public projects, except for smaller ones.
We have seen teases in Link Between Worlds and it was said that the game had references to Majora’s Mask. The mask was of course seen in the house of Link and when you won the game and played in Hero Mode you found the journal of Ravio, which gave reference to a three day cycle leading to the worlds end.
Nintendo will more than likely redo Majora’s Mask for the 3DS. They did have a lot of success with Ocarina and Majora’s Mask was just as popular. For now we are going to have to wait for the E3 in the fall.