Having Majora's Mask on 3DS with similar assets just makes too much sense for them to wait for the next handheld. They were originally on the same console, so I feel that it would be unfair to Ocarina of Time if the other N64 game got a different treatment.
A proper remake on the Wii U is also a complete waste of resources if you consider the changes they'd have to make for it to look great on the big screen, it doesn't have the timeless style of The Wind Waker, after all. Ocarina of Time 3DS was a smart remake, updating aspects that really needed it while not doing too much to textures etc. that weren't overly important.
I agree with SuperLink that I could easily see Majora's Mask 3D announced later this year (perhaps after Hyrule Warriors is out) or sometime next year. It wouldn't really impact a new 3DS Zelda, either, if Grezzo handles the remake again with supervision of Aonuma. With so many assets already updated, they also wouldn't have to spend too much time on it.