First the good stuff:
The animation is stunning, the 3D and 2D integration is some of the best I've seen. No corners were cut here.
The sound track is fantastic, it flows together and the surround sound is used well.
I enjoyed the story, it's a well trodden track but nicely done and not at all heavy handed.
Second the (not too) bad stuff:
I have the feeling they either spent too much on the some of the opening visuals or someone decided that it had to be exactly the length that it was and no longer. I shall explain in spoilers.
How come they are suddenly calling the ALBERT, Fi Fi, I imagine it came from the noise he made, but the name just appeared out of nowhere.
They go from hiding from Duke Red's henchmen to meeting Atlas the Revolutionary with nothing in between. It's not a show stopper, but it does leave you with a sense of Huh?