I can't believe I forgot about Okami.

That's a great example of a stylized game that is well done.
Comix Zone... yeah, the difficulty on that is crazy. I tried it out on the Genesis collection and couldn't get very far. I like the concept, but it seems more like a "memorize the path" game than anything else.
The art style for Wind Waker is definitely a big change to the Zelda series. If you can get past it, the game's quite good... but getting past the art can be hard. Given how poorly the art style has been received overall, I'm surprised that they're sticking with it so much. Minish Cap and the upcoming game, Spirit Tracks, also use it.