The Wind Waker presents a new perspective on Ganondorf. Never before or since has his character been so well developed. Rather than a figure hellbent for power and the pursuit of selfish ends, he is portrayed as a pensive man weary of his past transgressions and not really itching for a fight. Even when Link approaches for the final battle, the former Dark Lord seems hesitant to attack and wishes to negotiate. Ganondorf's defeat in Ocarina of Time and sealing in the Sacred Realm, definitely soured his thoughts regarding war, death, and destruction. This is a clear juxtaposition to his figure in Twilight Princess where he shows no hesitancy in making his power known and enforcing it. I don't necessarily believe Link can be viewed as an antagonist in the Wind Waker, however, the pity the player feels for Ganondorf clearly means the developers over at Nintendo accomplshed a significant end.
Cfrock said:
Even if Hyrule was restored, the people who ended up living there would be made to suffer greatly at the hands of Ganondorf. He's already subjecting The Great Sea to pain and suffering by spreading monsters and kidnapping young girls.
His only reason for restoring Hyrule was so that he could have the kind of power he once held. He isn't trying to restore the kingdom to its former glory for the good of all people. His motive is purely selfish and evil.
I disagree. As I stated above, the series of events following Ocarina of Time completely altered Ganondorf's perspective on life. No longer was he a cruel and heartless antagonist with expansionist desires but rather he sought to return Hyrule to its former glory even if he did not do so along completely moral lines. Also, it's worth noting that in The Wind Waker, Ganondorf strongly refrains from plans which threaten to interfere with regular civilian life. He may not have had the characteristics of protagonist, however, he definitely was not your traditional skull and cross bones type of villain.