It had the best character interaction, and makes you motivated to explore around. No, by this character interaction I don't mean Link conversing with Midna, and her splendid character developement. That is forced. This type of interaction is mostly optional, and yet, people feel as if they must talk to everyone. It makes the story more in depth. As for exploring, right at the beginning you are forced to explore Clock Town. From all the people, sections of the town, and overall "colors" of the story, you can tell that there is a lot to explore. This compares better to
TP in my opinion. I just wasn't motivated to explore whatsoever. I just focused on getting through the game because the characters were so boring to talk to.
This is what I saw in the innovation, more so than gameplay and story.