Take the frog side quest. Most players are going to try to start this sidequest as soon as they see it, but you can't complete it until you've got to a certain point in the game. In any other Zelda, this wouldn't matter. In MM, it matters a lot, because you end up wasting your time on a side quest when it turns out you can't complete it and you have to redo the whole thing again. That means finding all the frogs again, including doing minibosses possibly for the third time. It's annoying, repetitive, and tedious. Or take the sword upgrade side quest. In order to complete it, you have to beat the Snowhead temple on the first day. Any new player isn't going to to do that, so if they then decide to actually explore and discover things, and to do the Goron race and upgrade the sword, time and money is completely wasted because it's impossible to permanently upgrade it. You have to reset time, redo a boss battle you've already done, watch a cinematic you've already seen, spend money on a powder keg to blow up a rock you've already blown up, win a frustrating race you've already done (although it feels much easier in the 3DS version, maybe that's just me), buy a sword you've already bought for 100 rupees you've already spent, just to upgrade a sword you were one step away from upgrading half an hour ago before the game decided to articially punish you for not exploring and doing things in the exact way it wants you to.

My three biggest problems with the original majora's mask were the controls, waiting around aimlessly for sidequests, and constant repetition. The first two things have, in my opinion, been vastly improved on. The controls, at least for Goron and Deku link (haven't got to Zora yet) feel much much smoother and the improved song of double time gives the player much more control. But that frustrating repetition from not exploring and discovering in the exact way the game wants you to is still there. Frankly I'd rather have my hand held over when exactly to do things, like in SS or TP, than to be unfairly punished for doing things myself but at the wrong time. I feel like I can't explore properly until I've done as much of the main quest as possible, lest the game punishes me by making me redo what I've already done. As a sidenote, I wasn't much of a fan of the temples in the original MM (having not got to the stone tower temple), and I'm still not much of a fan of them here. I think the temples in MM are pretty comfortably the worst of the 3D Zeldas. The sidequests, though, at least when you don't have to repeat things, are great, and I don't think the bomber's notebook changes have made things too easy, as I feared it might.

New Look:
This is really amazing because the new fangled pretty graphics do not take away from the original mood of the game. This game is all about atmosphere, and none of it was lost. In fact, id argue that the atmosphere is amplified by the new graphics. The game feels a little more mature, but still whimsical. Link has more facial expressions, and everyone feels so dynamic.

Bomber's Notebook:
Im in a love/hate relationship with the new Bomber's Notebook. Not only was i left scratching my head as to why the Happy Mask Salesman gave it to me, i was also wondering why Jim doesnt challenge me again for it. I dont....i dont know. That was weird. The weirder part is that everything ever gets recorded in that thing. Bombers themselves are accosting Link and telling him stuff that hints to sidequests. Why...? That, and when you complete one, the game interrupts so the event gets recorded in the Notebook. This is kinda tedious and unnecessary. I get that they put this feature in so people could keep track of the junk they did in case they go through a lot of 3-Day Cycles, But its kinda annoying when the game interrupts to do this, instead of an unobtrusive ping. <.<

Theres shop owners and people being recorded in the schedule portion that neednt be there. Again, i see why this is a thing, but alas, im not exactly a huge fan. What i AM a fan of, is setting the Tatl Alarm. I havent used this yet, since i really memorized most of the major sidequests' times and junk, but the fact its there, is pretty awesome. So in case you go dungeon crawling, but need to meet Romani for some Mi-Go squashing business at the ranch, Tatl can remind you about that. The layout of the Ongoing Events, Rumored Events, and Completed Events is not exactly great though.

Weird Changes:
Some changes are just bizarre and im not getting the logic behind some. The logic behind the save stones being everywhere, however, is something i can grasp. Im ok with that, despite it being a tad clunky on screen. Song of Time does not save anymore. But its ok, cuz theres save points everywhere and they are not like the originals where its a one-shot save. One thing that was weird, was the Bank being behind the Clock Tower. Whats up with that? *shrugs* I just...ok. Sure, it makes the behind the Tower to look nice and like a park, its just weird.

Kaepora Gaebora is waiting for you right as soon as you enter the swamp. While his speech and the Song of Soaring is the same, the location strikes me as odd. Before, he was on a ledge on the way to Woodfall proper. Maybe they felt that location to be too out of the way? It wasnt cuz you couldnt miss it either way. Whatevs.

Once you get the Pictobox (which will photograph in color! woo), the first person view button changes to be assigned for the Pictobox. I reckon this is a thing because of the n3DS controls and the new c-stick being the free camera option. But im playing on an OG 3DS, so if i want to first person view (which im doing a lot of just to look at new details), i have to click on that Pictobox. Not a big deal, seeing how the Pictobox crosshair thing disappears after a second, but its a thing.

When doing the Kafei/Anju quest arc, Curiosity Shop Man is available to visit (where Kafei was hiding) as soon as the third day begins. Madame Aroma, you will have to catch her at the Milk Bar before the night. She will be there early in the day. Weird~ Also, you cant get the key to the room in the Stock Pot Inn like before, unless....Anju mentions a Goron Guest. Weird.

Fishing Spot(s). I dont get it, and im not sure why it exists. What is the reward? Why is it there? Why...I dont know. I just this one of those changes im really scratching my head over.

Im sure theres more, and ill note them as i keep going in the game.

Weird But Good Changes:
There appears to be changes for the sake of it, but like, not all of them are just weird or bad. Some of them are nice. The monkey at Woodfall will approach you when you get to the Deku Palace instead of after saving Koume. This makes more sense. Someone mentioned the platforms in Woodfall and Deku Palace not moving until you land on them. This is actually a positive change imo. Why? Cuz its an Anti-Frustration Feature. While it does diminish some of the dexterity needed to land right, i sure prefer not messing up. Also, you can aim really well with your Deku Nuts while in the air. Neat. Deku mask also has a nice crosshair you can aim with for the bubbles.

Goron Link, you dont have to hold A to roll and stuff. You push it to roll up and then go from there. Thats really cool. The Great Fairy in Woodfall expands your Magic Meter. This struck me as weird considering that was the Snowhead Great Fairy's job, but im not complaining. Thats gonna make my life at the Goron Races a lot easier. Since i usually waited till i got the Hookshot to do the Snowhead Stray Fairies.

The Song of Time. Can i talk about how freaking amazing it is to be able to choose the hour you want when playing Song of Double Time? Holy freaking shnikies thats awesome!

Certainly makes some quests a lot less of a pain in the bum.

The boss of Woodfall Temple was actually fun to fight versus being boring.

You can catch Sakon and the Curiosity Shop Man talking if you manage to wander into the Curiosity Shop at just the right time...Its pretty clever. Theres a really cool little model of Clock Town in the Mayor's front office. Nice touch.