You know, I never thought of it that way. Because there have been many OoT2D attempts here it is odd to think that Majora's Mask would be that much different in terms of implementing it in 2D. Also, in regard to tile work, I would think that it would have less than Oracle of Ages and Seasons as Ages involved significant time travel and Seasons had well seasons. Majora's Mask time travel involved just days. Link's transformations wouldn't be that bad either - most of the masks don't do much and the transformations cannot do everything.
I guess my vote goes for Majora's Mask then. If it gets to be too much and too many challenges present itself, because the engine is separate, it is not as if changing the game would be that difficult either. Majora's Mask seems like something good to attempt - there have been some MC themed Majora's Mask work made over the years too that I have on my old computer.