I think Ganondorf seems more powerful and seems to take notice that you're a threat instead of waiting until the last minute to be like "Hey! He's trying to kill me!" like Majora. (That's what Majora seems like anyway.)
I truly have only played Majora's Mask once for about 10 to 15 minutes, so I probably wouldn't know too much about Majora. But, I have done my share of research here and there to know that Majora does not really have a background. Even though Majora showed up in only one game, Nintendo probably could have revealed more about Majora's story and such. I don't really care for under-developed characters. This may be because I haven't played enough of Majora's Mask to know much, but it seems to me that Majora is just some strange "thing" lusting for control of something. So it decides to drop the moon on Termina for no good reason except the fact that Majora had the opportunity to do so.
The thing about Ganon is that he is not just a villain. He has his backstory and is what you would call a "round" character. Majora, on the other hand, was a "flat" character. So, I am aware Ganon may have appeared many times, but each time, it helps add a bit more to him. The depth he has makes him more interesting and... well, better. At certain points, you could see both a good and bad side to him, but he gets corrupted by his lust for power... His story is just so much better, and is obviously much more powerful.
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.