Nope, I think it's a real smart and well thought out story in general. I think the interesting thing about Majora's Mask is how it has a very deep backstory to it which you can't exactly tell from just playing the game once or not paying full attention to what everyone has to say.
I mean you think it's pretty silly that it's just a Mask, but that Mask is a demon. It's quite funny, it's only a "mask", yet it's probably more evil than Ganondorf, isn't it?
I mean Ganondorf didn't kill everyone, people were allowed to move to Kakariko and stay there, but, he didn't take his time to ruin everyone's lives.
Yet in Majora's Mask, so many people's lives around Termina have been shattered. Kafei being turned into a child and being put in shame, having to hide from the woman he loves. Cremia losing her sister, or if she doesn't, having to act all happy for her when she knows they're going to die. That Deku butler that lost his son because Skull Kid turned him into a trunk, Lulu's eggs being taken away from her (basically her children being kidnapped), the Deku King's daughter being kidnapped, the witch being hurt and even dying if you don't save her, right infront of you (if you talk to her on the second or third day, she replies at first, yet then says "...." and lays with her eyes closed), the little girl in Ikana with her father being turned into that creature, and having to act all mature to protect him, even though she's like 5. And well, in the end, he will kill every person and race in Termina by having the moon fall on them.
I could go on for ages, it's filled with mature, tragic stories, which are covered up well to fit a child's gameplay without them really realizing the sadness and deepness of it all. Other Zelda games are dark, but Majora's Mask is dark in it's own respect, and differs from the other one's completely in my opinion.
I also love that there's a lot of backstory to some of the things that happen, mainly the Ikana one, with how the Stone Tower was built to reach the heavens to show the Goddesses they were more powerful than them, defy them, yet it was flipped upside down for them to go to hell instead. And the "subtle" details in it such as how the triforce is strategicaly placed on the crotch of the those big blocks which are found around Ikana, as well as other things you can find there. I also like how you see that, if what I read was fact, that when they reached hell, that's where they found Majora's Mask, which was a demon, and they worshiped it, which is why we find images of Majora or carvings of it in temples and all.
I like that there's a lot of story to the game, yet it's not shoved in your face as you progress, instead you must look for it and link things together C:
, but I am inclined to disagree. The mask itself is possessed, and that evil flows through whoever is wearing it. Because the Skull Kid wore it, the evil flowed through him and made him possess the most destructive and biggest object he could; the moon. The four giants already existed to keep the moon at bay, but since Skull Kid was possessed he sealed the giants away. Finally, when Link rescues the four giants, the evil of the moon (from the mask) pulls Link into the "eye-of-the-storm" per say, where he battles the actual mask. And since the actual Mask is possessed, it doesn't need a host to use its evil. So basically, the main villain is Majora's Wrath. 
