That's a big question!
Well my dear ZeldaDungeonee. The reason Majora's Mask is considered the best game in the franchise by most Zelda fans ( Fans who've played a lot of the games I mean ) is because there's so much to do. While if I said that were the only reason why it's considered the best I'd by lying.
Firstly ... Majora's Mask has a great story. It's a much more intuitive and powerful story and it just grabs you in and doesn't let go. Sure when you think about it it's not that much of a story but, think about it a bit more and you'll see that it's a lot bigger than you think and there's a lot more to it than most other Zelda games. On top of that all the sidequests in the game also have stories of there own, obviously. All that adds into a game with so much going on story-wise that it's hard not to love! The Anju and Kafei quest, Romani and Cremia's story. Those big ones obviously have neat stories and you may overlook the littler quests but come on an invisible guy who's hurt! That's pretty cool too.
Now more onto sidequests. If you're not a fan of sidequests Majora's Mask will make you a fan of them. On a game that focuses on sidequests, the sidequests need to be done RIGHT. A lot of zelda games do them right, but some others do them wrong. Majora's Mask does them greatly. You really care for the characters you're helping! I actually feel a connection with the in game people and not many games make me feel that way. After helping them all you'll see what I mean. The way the time works with the sidequests is genius to say the least!
Speaking about the in game timer! That is another great thing about Majora's Mask. I don't want to hear anybody complaining about the in game timer because there's nothing to complain about! Slowing down the time with the Inverted Song of Time gives you 3 hours to play. That's more than enough to complete any dungeon at all. The way the clock works is amazing. I loved it when I was 5 and I love it now. It can be nerve wrecking and could ruin your entire run through the infamous Great Bay Temple or the rugged and deadly Stone Tower Temple but I'm sure you'll be able to overlook that. It works so well, and makes the game a lot more involved.
Finally we get to the dungeons. This game has three of the greatest dungeons in zelda history. There are about 6 Dungeons in total and four dungeons with BIG BOSSES. The three amazing dungeons that stick out in my mind are the Woodfall, The Great Bay and obviously The Stone Tower Temple. I'm not going to go into too much detail as to why these dungeons are amazing but I'll give a brief explanation. The Woodfall temple is one of the best first dungeons in any zelda game and has good music. The Great Bay is a challenging one and keeps you on your toes wondering where those fairies are and it also has nice music. Finally The Stone Tower Temple.. well this temple deserves a topic thread of it's own just to explain it in detail but in short, it's very creative, very tough and has one of the best if not the best music in Zelda history..
Oh and speaking of which.. Majora's Mask also has one of the best soundtracks in any Zelda Game too!! Milk Bar, Stone Tower, Deku Palace, Overworld, Clocktown day 1,2,3 , Area Theme for swamp, mountain, bay and canyon are all great! and so much more!
You NEED to play this game to call yourself a hardcore zelda fan. It's probably not the best one to start with as it is somewhat challenging but, it's a required one to play and beat if you want to even think about calling yourself a TRUE Fan..