He's a sad and interesting villain, from a game with what was initially sort of a cult following that seems to have grown into a much more mainstream appreciation. It may never hold a candle to people's perception of Ocarina of Time, but the game he represents is one of the most interesting in the Zelda series. Furthermore, his partnership with the mask he wears has the potential for a very interesting moveset. Beyond that, Majora's Mask has never had a proper representative in Smash; Young Link is based on his OoT appearance.
For me, it's a combination of all these things. I love his character, his moveset potential is excellent, and I want his game represented through more than just a stage, because it's my favorite game.