The series came before the movie -- and I am told that the manga came after the series as well. Usually the manga comes first. The movie was really to satisfy series fans who wanted more. But they really could not do much with continuing the series' storyline because of the way it ended. It was a good ending. Let's leave it at that for now. Anyway, that is probably why they came up with an entirely new storyline for the movie. Although they could have done the storyline from the manga, which is along the same lines as the series, but ends quite differently.
What I would have like to have seen is a prequel to the series. I would like to have seen how Eureka was discovered and her development into a heartless soldier. I would like to have seen Talho's relationship with Dewey, and exactly how Holland turned rebel. It would end where the series begins -- when Renton first meets Eureka.
You probably don't know what I am talking about, since you have not seen the series. I will say no more. I may have said too much already. But see the series.