Well, besides the fact that Ganon/dorf is a little overused in Zelda games, I find Majora interesting because she's somewhat unique as opposed to Ganon.
Ganon's goal seems to always be to get the triforce and take over the world.
A pretty common objective in villains.
Majora, however, has no interest in taking over the world. She instead serves as a metaphor for unchecked emotion (in my opinion) and its self destructive nature (destroying the world with a creepy moon), a welcome change from Ganon's representation of lust for power, the villain archetype.
Majora is also unique to me because, at least for most of the game, your only image of her is the mask, and even at the end of the game, you don't really see Majora herself, but only her wrath and incarnation. This ties into my metaphor point, since Majora doesn't really have a physical presence the way emotion doesn't.
Also, the image one thinks of whenever they hear the name Majora, the mask, is such an incredible image. Its huge eyes look like they're looking inside you.
Majora's goal, motivation, deeper meaning, presence, and appearance, maker her the more memorable villain to me.