I agree with Darkest Link, I don't see why Nintendo would want to do this. Yes, it would please the small but very vocal group of people who actually want it, but from a business perspective it would count as a loss. Even if they already have the base code from OoT3D, it still takes a significant amount of investment, both financially and monetarily, to remake MM with the improved graphics. And with the way Nintendo is going, that's not a smart move in the long run. They need to focus on creating new games for their franchises (or even better, creating all-new franchises for the younger generation to latch onto like we all did for Mario and Zelda and whatnot) than remaking older games that a small but vocal fanbase are clamoring for.
And really, why does Majora's Mask NEED to be remade? The game still looks really good. It can still be played in its original format just fine, those who want a remake already own a version of it, why is a remake necessary?