I've made suggestions in other threads, but I'll say them again here, I guess. If they change anything, they should let you switch back and forth between shields... I know that's random, but I've always wished you could do that. Not that I will care if they don't have that either, it's really unimportant, it's just the only game-play change I would want XD As far as other things go, they could use the touch screen to let you make your own notes in the Bombers' Notebook, I feel that Majora's Mask could benefit from some in-game note-taking section, and even more so if it's going to be on a handheld. I also really hope they put the timer on the lower screen so you can see the beautiful world of Termina better, the original game has such a messy screen.
But any changes would have to be very minor, I don't want them to change the main game besides the graphics and controls like with Ocarina of Time 3D. They really didn't add or change much as far as game-play goes with Ocarina of Time, so they don't need to change anything in Majora's Mask either. And... I really don't see them making a Master Quest for it, if anything they would bundle it with a side-game of some sort rather than a Master Quest. Not that a Majora's Mask Master Quest wouldn't be great, but the only reason Ocarina of Time came with it is because it already existed. I certainly wouldn't want something that was thrown together just to add content to the cartridge.