Overall I felt that it was a much more enjoyable experience than playing it on the N64. I personally grew up playing Majora's Mask; it was the only Zelda game I had until Wind Waker, as we had sold our OoT copy (which I missed dearly as a child), so Majora's Mask was all I had to play Zelda-wise. I would spend a long time just trying to figure things out and it was the game that I really got down to earth with, and it was only until I picked it back up around the time I hit middle school did I realize how much I loved the game.
Anyways, what I am getting at with this is that as a child I had trouble keeping track of everything, and we even had a guidebook. The game made it very smooth with making sure you didn't forget what you were doing, or that it made it easier for what you have already completed, and what areas you have already cleared. Nothing was more bothersome as a child as when you did circles over the same area a few times, and you already got the item, or the heart piece, or whatever it was that I did. The game made it possible so that you can actually multi-task and not waste time, all without getting rid of the challenge that was set in place. There was only a few things I had to look up in order to complete, such as getting the 7th bottle (which was actually a cool addition because it made use of the Gorman Mask, which was useless other than at the end for the Fierce Deity Mask in the original).
Everything just felt a lot smoother, and it didn't feel like I wanted to ragequit a lot of the sections. It still had it challenges like in the original, but at least the challenges were something dealing with the gameplay and riddle of the game rather than based on how well you are able to pay attention and remember what the hell you were doing just 20 minutes ago. I did find myself able to multi-task the hell out of the game, and actually going to like the last minute of a 3-day cycle before going back in time. I think Pikmin 3 made me that way.
I just want to say that the Song of Double Time's change in this game was probably the greatest thing to happen to this game. I actually could stomach the Anju Kafei quest without having to spend half the time waiting for time to slowly move. I only had to ragequit the game at one point, which was on this quest, and that was because I accidentally failed to get the Sun Mask because I pushed the block the wrong way. Thankfully you can save your game without going back in time, which didn't bother me, and in fact I enjoyed that change as well, though I rarely ever used it.
The boss changes were moreso good than they were bad. Odolwa was for the most part the same, but actually incorporating Deku Link into the battle, which I thought was nice. Goht was the one that I do think shouldn't have been changed, and was a pain to deal with having to stop, take off the mask, shoot fire arrows, and then put back on the mask, which affected the flow that the original battle had. Gyorg was definitely a lot easier than in the original, but I'm fine with it since I don't have to worry about getting eaten after attacking him. And the way they incorporated Zora Link was a lot better than in the original. Twinmold definitely was a battle that I completely loved, and man was that one of the best boss battles in any Zelda game ever. They made Twinmold actually a menace, and made you get to wrestle the red one after you destroy the Blue one, and it was just tons of fun. I can't say much for the Majora battle, since I used Fierce Deity, but I'll have my opinions when I face him without the cheat mask.
The Zora swimming downgrade was a bit tedious, but I liked that you didn't have to jump out of the water onto platforms like you had to do in some of the temples. However, let me just talk about the Gyorg Moon challenge. That piece of shit was just the worse. It wasn't even the fact that it was timed, or that I would miss the jump; it was the fact that missing the jump and not being able to swim back made you have to restart the entire thing, and it was just like "good on the first section, good on the second section and-damn it, missed the jump in the final area!" It really sucked because I wanted the Piece of Heart, and I ended up in the end before I meant to, so I had to exit the entire thing and re-enter the game, which was just salt in the wound. I mean, I understand that it wasn't that challenging in the beginning, but they literally had to take my hatred of the Zora jumping and raise it up 5 knots.
So, with all that said, I think that most of the areas benefited greatly from the changes, and made the original seem so outdated. There are some areas that didn't really need a change, or that areas that did need some change but didn't get, but they were minor and not that close together. I think that it definitely was an amazing game, and I did tear up when I got Anju and Kafei reunited, as well as when the Skull Kid realized that the Four Giants still thought of him as their friend. This game was definitely fun, and obviously from the fact that I 100%'d it in 3 days, I could not really even put it down.