i think that the main theme of wind waker is "what kind of world are we leaving to our children?" and it's pretty much synthetized by the character of the king of red lions. it's a very "japanese" theme, since i believe much of the modern japanese culture is influenced by the enormous shock of beeing attacked by a nuclear weapon, some sort of armageddon on a lesser scale. it's a common theme on a lot of anime and manga.
the drowned hyrule is a metaphor for a post-holocaust word. the king and ganondorf are the ones guilty for that distruction, but while ganon lives in the past and still wants to rule hyrule, even if it is an empty, ruined, ded world, the king, full of regret for what happened, wants to give the children another chanche, a seed of hope.
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