To be fair, tons of people like myself have been clamoring, and LOUDLY, for Majora's Mask 3D. I doubt Sakurai is completely ignorant to the massive cult popularity of Majora's Mask. Skyward Sword...not so much.
There's a few differences, I think, though: Majora's Mask is an under-appreciated N64 title overshadowed by OoT and the GameCube. Majora's Mask is loved for quaint and uniqueness, but it's extremely outdated now. So, naturally, everyone wants a remake.
Skyward Sword, however, was released two years ago on a console still available. No one wants Skyward sword because
everyone has it. Plus, it's got tons of attention, both before and after release. And, most of Skyward Sword's popularity came from not the game itself, but the story and characters in it.