Best 3D Zelda to date.
The key distinguishing factors are:
1. A Groundhog's-Day-like, 3-day timeloop. 2. A shape-shifting Link, which can change into various forms.
3. A setting similar in layout to Hyrule, called Termina, which is supposedly an parallel universe type of deal with Hyrule.
I think the shape-shifting makes this game. In other Zeldas, Link is kind of like a medieval James Bond or Batman, with all these gadgets and toys to help him out. In Majora, the gadgets are still there, but now you have special abilities based on your gene-splicing state (form). This makes the game more fun. My only complaint is that there is no flying form, outside of the deku scrub's short-range helicopter.
The character's that make up the world are repetitive like almost all RPG-type games, but now at least there's a logical reason for it. It's nice that each character has their own life, and set of activities that they do during each "loop". It's very much like the movie Groundhog's Day. You should watch that before playing this Zelda installment. Some of the same issues are tackled. Boss design is outstanding. I especially loved the snow temple boss. Each temple is themed to the area's archetype, and has a boss you can only defeat using the form you attained in that area.
The form-changing masks are not the only masks that are fun or useful. Some other masks have certain properties, like animal mind-reading, stealth, speed, and giantism. As the game's name implies, this game is all about the masks.
A lesser-known improvement over Ocarina of Time was the original field music score. Fortunately, the backlash for this omission was huge, and Nintendo is likely never to leave it out again in future Zeldas. To me, it is one of those things that defines the Zelda playing experience.
Overall, this game deserves to considered among the great Zelda games, even though the dungeon and boss count was comparatively small. It made up for it in story quality, side quests, and overall gameplay. It shows a Zelda game doesn't have to be all about dungeons and bosses.