Hmm... I must be one of the few that never expected any more from the villains. I do admit that the motives are rather clichéd most of the time in Zelda games, but I'm starting to question wether that ever mattered in the first place, you know? It's pretty well known that Zelda is supposed to have a somewhat conservative air in its story, like a fairytale. I know that might not be a good excuse for how lacking they are sometimes, and they border on shallow if their interests don't really go beyond obatining a power to rule the world. Majora was an interesting twist, since it was mainly a sadistic maniac whose goal was making everyone suffer indiscriminately.
I also thought Ganondorf had interesting motives in Wind Waker, where there was clearly a lot of personal gain involved. That world he was looking to control meant more to him than just "Me-land", like he was winning a life-long battle against the odds. As if his dialogue before the final battle didn't make it clear enough... (wow, I just noticed I'm bringing this one up a lot)
Ganondorf said:
My country lay within a vast desert.
When the sun rose into the sky, a burning wind punished my lands, searing the world. And when the moon climbed into the dark of night, a frigid gale pierced our homes.
No matter when it came, the wind carried the same thing... Death.
But the winds that blew across the green fields of Hyrule brought something other than suffering and ruin.
I coveted that wind, I suppose.
I notice I've been bringng this one up a little more than often lately, but that's because I really think this part made Ganondorf as a villain and
a character for me. My point is, I don't really think the villain needs a complex, or even deep motive. I've always thought that his goal has to mean something to him, and that devotion has to be clear and convincing. I've never thought villains were too different to heroes in that sense, they all look for something and follow it with utter passion. I think that would lead to Link himself having a strong motivation in many ways. I think they both need one to be well developed.
You could say that I'm easy to impress, but I never really thought that kind of villains who just want to rule the world were really bad. I might just be the kind of person that the classic approach was made for, after all. But I still stand that they have to have a motivation as strong to get their goal as Link has one to stop them. I guess it's that clash between sides that makes the apparently simple dicothomy of good and evil these stories seem to present all the time.
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I know that this might be controversial, but I would love to see a motive of genocide. Maybe a Gerudo, maybe not, but someone who wants to rid the world of Hylians.
With all that said, it would be interesting to have one with a darker motivation like genocide. I'm not sure if it would be that controversial since implications wouldn't have to be that direct. In fact, I've heard more than one person who thinks that the citizens in the Market in Ocarina of Time are the re-deads you find when you go there as an adult. I have my doubts about that, but I guess it's safe to assume that they were alive at some point.
If you mean a straight out genocide, that would be... interesting to see. I can actually see Ganondorf pulling that off, if his jealousy of Hyrule's fortune was really that strong, I bet he would've done do anything against the people in it if the writing had called for it instead of him just wanting the land. Motivations like that can go a long way in the villain's actions depending on how they are used.