The fact that to make Majora's Mask on the 3DS would take a lot less time and energy. Plus they already have the models from Ocarina of Time 3D. And if Ocarina of Time wasn't remade onto Wii/Wii U what makes you think Majora's Mask will be?
The fact that Wii U wasn't yet in a good enough state/maybe not even announced yet at the time Ocarina of Time 3D was announced?
Also that OoT3D was probably a launch title to promote what the 3DS is capable of.
Seems kinda counter-intuitive they'd make a super-HD trailer for something and only have it in a much less HD form on a handheld when it was originally on console anyway and then make Pikmin 3 on the Wii U and announce other things as well for it.