The thing I notice most people saying is that Ganondorf had a major impact on the story. You really could've replaced him with anything though. Zant could've gotten his power from some supreme item that bestowed great darkness to Zant. Zant could've been the final boss after you got the final...
Ganondorf to me was a rushed addition to Twilight Princess. It is not that he shouldn't or should've been included, it is that he was horribly inputed. He is rushed into the story after the near end of the game after you think Zant is the main villain. It was a plot twist that did not work in...