Zelda being revealed in Windwaker is probably interpreted by many as a coming of age moment(girl growing into woman, assuming mantle of responsibility, yada yada yada), but instead is Nintendo making a statement against the restrictions and impositions of forced gender roles.
Before the reveal, Zelda's character is pro-active, a strong figure, independent and actually Link's guardian. She is an outdoorsy tomboi, wears pants, has a tan, commands respect from the men around her, and lives a carefree, idyllic, self-fulfilling life.
Immediately after the moment of the reveal, Zelda opens her eyes and is shocked to find herself drastically feminized. She wears a dress. She wears heavy make-up (especially considering she's a child of what? 12 years?). And to seal forever her fate as a disenfranchised barbie doll, as a damsel in perpetual distress, and, most importantly, as "a woman who knows her place," Zelda realizes that she's the ultimate little girl feminine fairy tale: a Princess. Zelda has just been Disneyfied.
Now, Princess Zelda is no longer pro-active. Now she no longer yields power. She cowers in the basement of the castle, hiding from the outside world she was once free to roam. Whereas before she could fend for herself, now she is completely reliant upon Link for protection, for support, yes, even for news of the outside world. She has become a prisoner of her new role as a female, as a princess, as a domestic ornament.
While Valiant's comic book adaptations of Zelda from the 80's and early 90's showed a modern woman who was intelligent, skilled, witty, and often-times the hero of the story (unlike the classically bumbling Link), and Miyamoto's Ocarina of Time Zelda was a shrewd, resourceful, cross-dressing proto-feminist, Aonouma has crafted a far more prescient and bleak existence for a character who has come to embody not just the Legend of Zelda, but indeed the Legend of All Free-Thinking Women.