It was some years ago when Nintendo said that they would look into a remake of Majora’s Mask and bring it to the 3DS. At this time they had been deciding on two Zelda games. These were Majora’s Mask or a sequel to Link to the Past. Nintendo went ahead with Link Between Worlds. Which many people said happened to be the second best Zelda game ever.
The team over at Nintendo that work on Zelda is huge and as such they could work on two games at one time. Last year they did this when they worked on Wind Walker HD, Link Between Worlds and Zelda Wii U. Zelda Wii U is the biggest game that the company have ever developed.
Maybe Majora’s Mask is being worked on by Grezzo. They were responsible for Ocarino of Time on the 3DS. They know all about the core system and other than small ones, they have not worked on public projects.
In Link Between Worlds there have been teasers and these made reference to Majora’s Mask. We saw the mask in Links house, plus when the game had been won and the player played through in Hero mode, the journal of Ravio was found. This told people about a three day cycle which led to the Worlds End.
Fans have said that Nintendo will redo Majora’s Mask for the 3DS, after all Nintendo did enjoy success with Ocarina and Majora’s Mask was popular. For now fans are going to have to be patient and wait to see what the E3 brings this fall.