I'm just going to plagiarize stuff from myself here since I doubt anyone reads my comments in my subjective anime score table.
This is a tough one, but to be very frank, the second season has almost nothing that makes it stand out amongst hundreds of other anime that comes out. Some of the most beautiful background shots are the ones created for the first season and then simply reused, so I couldn't give it 5-stars. Newly created images aren't nearly as good as the ones created for the first season. The story is somewhat intriguing, but what made the original so special was that it was a fairytale to the core with just a hint of ideas to help the viewers think a bit more about the story. Second season breaks the image of the fairytale.
Skip the next paragraph if you have not finished watching the entire 2-seasons of the anime.
And I figured out the secret about Tutu's pendant way too early. See my "Princess Tutu DVD 4" listing. Regardless of whether I figured it out early or not, I think the whole ending could've been handled better. The only thing I like about it is the fact that Rue got a happy ending. Heck, even that is just a personal thing. I just wanted Nana-chan's character to be happy.