needed to add a mechanic to slow time down
The devs actually thought of that. There are two auxiliary time control songs. One slows down time by ~50%, the other jumps ahead to the next dawn/dusk. MM3D revised the latter to allow to jump to any top of the hour across the next 12 hours.
Any of the scarecrows around town teach it to you just by talking to them, but they do so by describing the songs, not teaching you the notes
The way I think about Majora’s Mask as a Zelda game is that in addition to exploring the physical world, you’re also exploring time. That does necessitate “backtracking” by forcing time resets and a lot of waiting around if you don’t immediately know what you can be doing in parallel (though the two time control songs make that part easier).
With the exception of the dungeons themselves, the game typically fast tracks getting you back to where you were when you just reset. Some mechanics like that the game forces on you pretty quickly (song of soaring fast travel), others it lets you figure out on your own (dungeon boss instant warp after beating them the first time).
Side quests can be a bit more troublesome to deal with if you have to reset part way through, but each interaction point that you have to go through offers you another way to handle things (or to not and let another sequence of events happen).
To your last point, the game really throws refillable items at you in the overworld, so a lot of times you can skip that (I’m not saying stocking up doesn’t take forever on reset, it does. You just don’t always have to)
All in all I really love the time mechanic of the game and that let’s me forgive some of the other flaws of the game. If it fell flat, then yeah I can see how the game quickly becomes a chore. But I adore the game, hence the username
Whenever I replay OOT I never have a problem with Navi. She rarely hard interrupts, usually just a short tone and flashing C button that goes away after a few seconds. The voice lines only trigger if you press the button to call her, in most cases the hints she gives are genuinely helpful, and stays out of your way for the vast majority of the game.
Fi from skyward sword though… Far worse because she does interrupt gameplay, often repeats what the last dialogue box just fucking told you, and takes several dialogue boxes to tell you what Navi would have taken one to do. I’m glad they significantly overhauled her interactions in the HD release but I’m still going to be hesitant to play that game again