Majora's Mask is the first Zelda game I've ever played, so I'd like to say it's the one I want remade. On the other hand, I've never played A Link to the Past, despite all the awesome things I hear about it. I'm indecisive, therefore, on which I'd prefer to see in 3D or HD—whichever Nintendo intends to design them in.
Perhaps the best remedy to this is putting one on the 3DS and the other on the Wii U. This would give fans of both games the opportunity to try them on either gaming device, and in a higher standard of quality than the originals, for those who look forward to aesthetics. If I were to guess Majora's Mask would likely go on the 3DS, following the steps of OoT 3D; and the ALttP remake would go on the Wii U.
The only foreseeable downside to this is the lack of new games. Nintendo's development team would have their hands full with the remakes to release brand new titles to the fans; and while many are hopeful for the remakes, everybody clearly is not. Many follow the franchise because of the fresh adventures that Link goes on every few years. So if both MM and ALttP were to be remade, it would be best to stagger their developments and release dates so that novel Zelda games could be squeezed in here and there, whenever it's suitable.