The save system isn't any more cumbersome than the one in A Link Between Worlds. It basically translates to playing a warp song to go to a thing and then save. And I don't see how anyone can complain about the stray fairies, unless they didn't have the Great Fairy Mask, or (even worse) are the kinds of people to just go "yeah yeah yeah I don't care whatever shut up" and mash the A button whenever a dialogue box interrupts their hamster-esque attention spans, and therefor didn't know the mask's function.
@Lady, Wouldn't a power failure wipe all your progress back to your last real save anyway? Unless you're the type of person who saves after every tiny little accomplishment (which you could be), you'd just be in the same boat.
And people who complain about the time function irk me. Of course it puts pressure on you, the world is ending. Termina is suffering from a literally imminent catastrophe. If anything, I love the time system. There is a huge contingent of newer games out there where you are supposedly facing off against some world eating Big Bad, but paradoxically, that BB is waiting for you to finish faffing about with literally every single side quest you can get your merry hands on before you deign to face them. What are they doing that whole time, having a wank? Meanwhile, that Moon gets bigger and angrier by the day. God forbid a game whose theme is "hop to it before the world ends" forces you to hurry it up a bit. The time system is more than the sum of its parts, that added tension colors how you experience everything else the game has to offer. Without it, no part of that game would have been the same.
And besides, the Inverted Song of Time and Song of Double Time are some of the easiest things to find in the game. If you didn't explore well enough to find out how to play them, then that's your own fault.
Anyway, sorry, I just had to get those off my chest. The most common complaints I've heard levied against Majora's Mask are its dungeon count, its main quest length (most people I hear from say they beat it about a day or two faster than OoT, and since it immediately followed OoT that was the most ready comparison).