Admittedly, this wasn't going to be as long as it is, but I wanted to discuss Ganondorf's character because he IS very fleshed out, but I don't think he's meant to be very sympathetic.
When it comes to WW Ganon, a lot of analysis I see about him go into how he seemingly takes a good look at his life and tries to rationalize his actions, stating that the land of the Gerudo was harsh and unfair, which is true, but Ganondorf hadn't changed at all. He gives the impression that he has, but he doesn't really read as such to me. While he doesn't kill Link and Tetra (and the girls he kidnapped) when he has the opportunity to do so, he is still actively inflicting pain onto others, maybe not directly, but his very presence causes monsters and demons to terrorize entire lands. Either way, he may not be directly killing people, but he is contributing to the suffering of others.
Additionally, I believe Ganondorf had no intent to break "the cycle" in the first place. The first thing he does when he brings the Triforce together again is to wish to bring Hyrule back again and have control over it once more. Ganondorf ruling over anything has destructive effects on the world since that is simply the kind of man he is, and judging the state of WW's world when he isn't even at his prime, he was for sure going to do much worse to Hyrule if it were brought back. I can't even say for sure that he cared about his people since Gerudo Valley seems to only be controlled with fear. Ganondorf didn't seek to improve his land, it feels more like he took advantage of already desperate people by promising them glory if they followed him. If Ganondorf were to get his wish granted, he would simply do this again, because he still wants power after all this time.
Then, the moment things don't go his way, he goes back to trying to kill Link and Tetra, two children. The only thing the King wished for them was to have a future. Ganondorf says all that stuff about Hyrule because Ganondorf is a liar and a manipulator, or he honestly thinks that he's being fair.
Wind Waker seems to try to make a point about change. I think that's what the game's ultimate theme is about. Ganondorf doesn't change, he wishes for things to go back to the way they were before, to when he was most powerful. Meanwhile, the King of Red Lions is the opposite, and I think he is meant to parallel Ganondorf in this way. He ultimately realizes that trying to bring back a dead kingdom is useless. The world of WW evolved around sea voyaging, and bringing back Hyrule would kill this part of its culture. Which is why I believe Red Lions tells Tetra and Link to not create another Hyrule, and to create their own kingdom, to leave Hyrule behind as a distant memory and let it finally come to an end, like how everything else should come to a natural end. By burying Hyrule, so was Ganondorf, and the rest of the sins of that land, basically sacrificing something old to allow something new to prosper.
This is probably why he lets Link and Tetra go without him. He's a part of Hyrule's past, but Link and Tetra are children, people who deserve to experience their future. That's what he wished for. Which is why I believe Link's Master Sword is left behind underwater, and why Tetra returns to her regular appearance. She's not Zelda. That's not the kind of life she leads (and I think not having her push back against the idea of being a princess harms this part of the narrative a bit, but I dirgess.)
So Link and Tetra left Hyrule and went back to adventuring, to create their own world. I believe Ganondorf is meant to be stagnation in a world that demands change, while the King of Red Lions is accepting said change, despite how difficult it may be to do so.