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Millennium said:
It's a series about a legend: many versions of what is, fundamentally, one story. In that story, Ganondorf is the primary antagonist just as Link is the protagonist. Why is there any problem with this?

Except it isn't one story. For example the Hyrule in LoZ isn't the same Hyrule in OoT. There IS a timeline, no matter how screwed up it imay be. I agree with the second part.