All of the reasons you gave about why Wind Waker is good are why Ocarina of Time has the best story. It's both traditional and non-traditional at the same time. The game starts off how you'd expect, but then after the "mini-climax" everyone hates Link because he was the hero who was supposed to save them and he just up and disappeared for years. Zelda actually gets off her ass and starts doing stuff herself in a superhero disguise.
That said...Link to the Past is still the best Zelda game overall. It's where the formula that later Zelda games became so slavish to was perfected.
That said...Link to the Past is still the best Zelda game overall. It's where the formula that later Zelda games became so slavish to was perfected.