If they do remake Majora's Mask (and I would give my first born son if it meant they would do it) I would greatly prefer it on the 3DS for many reasons.
1 - It wouldn't take long to develop because, as Ventus said, 3DS games are easier to make than HD ones. On top of that, you already have a working engine as well as sound files and even character models, not to mention all of the story and dialogue has already been written, so a lot of work towards it has already been done. Additionally, Ocarina of Time 3D was done by a studio named Grezzo. They would most likely handle Majora's Mask 3D as well, which means Nintendo would be completely free to focus on original Zelda titles.
2 - Graphics. We can all say they don't matter until the cows come home but we all know that they do make a difference. They may not be the most important thing in the world but they still matter. As much as Zelda in HD is no doubt going to be beautiful, Ocarina of Time 3D is easily one of the most attractive looking games I have ever played. It easily has the best, or at least some of the best, graphics on any handheld game ever and the main reason is the 3D effect. The 3D has such a huge impact on how good the game looks and seeing Majora's Mask in such a way is something I think I need in my life. I would rather have the two N64 era games be presented that way than have them look totally different.
3 - I don't know if people really do see Majora's Mask as 'Robin' to Ocarina of Time's 'Batman'. Majora's Mask is recognised as great and is appreciated all the more with time. Now that we are so far from the original release of Ocarina of Time, people appreciate Majora's Mask in its own light a lot more. Having it on 3DS will introduce it to a whole new generation of players. All of those young people who first played and loved Ocarina of Time on 3DS will be given the chance to experience Majora's Mask as well, and they'll probably appreciate it more because Ocarina won't have put stars in their eyes the way it did to us in 1998. The 3DS is Majora's Mask's chance to really shine like the beautiful jewel that it is, for us and for a new generation.
4 - The portability factor can't be ignored. Having the game wherever you go is one thing but consider the structure of Majora's Mask for a second. That three-day cycle puts your immediate objectives into focus. When playing, you often find you manage your time, deciding on which actions to make on the first day, which on the second, etc. That kind of compartmentalised gameplay suits portability perfectly. Playing the game, you think to yourself 'I will go and clear the path to Romani Ranch. That will take until the night-time'. On the 3DS you will think 'I will go clear Romani Ranch. That will take until the end of my bus journey'. More people will be more willing to take the game on the go because the time system emphasises doing smaller tasks. This will also help people get over the main gripe they had the first time around which was that very time system. Portability takes what was, critically, the game's biggest weakness and turns it into a strength.
I'd be elated with Majora's Mask on Wii U, of course. But if it were up to me, this wouldn't even be a choice. The 3DS is most definitely the better option for us and for the game itself.
