Wind Waker's one of my favourite Zeldas, in large part because of the story. I like that the Link this time around is just Some Guy(tm) who seems kinda lazy, but then the giant bird kidnaps his sister and he decides right then and there that no matter what he has to do or how long it takes he is going to have a giant bird skull to mount on his wall
I'm generally not a big fan of "the chosen one" or "fate and destiny" as plot devices - I feel like they take away a lot of agency from the protagonists. It's just not as interesting for the final boss to be fought "because it is your destiny" compared to "it's because he pissed you off." It's why my other favourite Zeldas are Link's Awakening and Majora's Mask. The quests in those games are also largely undertook by Link moreso of his own volition than any grand predetermined plan from the gods. And it's why I really like the Link in Wind Waker. He has to earn everything throughout the story, so his big confrontation at the end doesn't feel as much like "the big final battle that destiny has set aside for you" and more like an actual culmination of everything up to that point. And even after his own personal quest is finished, he still works to fight the good fight not because he was born to do it but because it's the right thing to do. I just like that.
I do kinda admit I wish the actual gameplay world had a bit more depth to it - the game had a lot of content cut and it suffers a little bit for it. But sailing across the ocean, hunting treasure, finding secrets, it's pretty fun. And the visuals are out-of-this-world, they still hold up today. I wouldn't mind if Nintendo revisited this concept again in a more modern title, and gave it the time it needs to truly shine.