LogFAQs > #985850139

So if I had to guess - and I'm sure Evening Dragon will correct me when I'm wrong - it's about the change to saving the game.

See, with the N64 version of the game, the only way to make a permanent save was to reset time back to the start of the three-day cycle with the Song of Time; you'd lose any progress you made on sidequests, any rupees or ammo you had on you, and the dungeon bosses would respawn, but you'd keep any heart pieces/containers, masks, songs, or major items (like the Bow, the Hookshot, etc) you obtained. However, you could make temporary saves at the game's warp points, which would last until the next time you turned the game on and loaded that save file, at which point the temp save would delete itself. Think of that as more like being able to pause the game and turn off your N64, then come back later and pick up where you left off. You'd still eventually have to save, but it was a good way to handle things if something came up without warning

In MM3DS, on the other hand, they changed it so you just make a permanent save at any warp point statue, and then added a bunch of secondary statues around the map (usually in sub-zones or at the start of dungeons/mini-dungeons) that can also be used to save the game, but which can't be warped to. All the Song of Time does now is reset the three-day cycle, which can be really annoying since you now have to go to the warp point in the central hub after going back to Day One to save. It's one of those changes where I kinda get where they were coming from - MM3DS is on a handheld instead of a console, so having to quickly save and quit out is potentially more likely to come up - but it also means that you don't have to worry as much about things going pear-shaped (a sidequest goes wrong, you run out of time), since you're no longer starting back over at the very beginning.