Its damn difficult to watch the movie after the series and try to enjoy the movie for its own sake. There are some gems here, like, as others have mentioned, the music and the art.
Though it isn't nearly as defined as the series', the world of A Girl in Gaea intrigues me; I found myself desperately wanting to know more about it and to explore it. For example, I don't remember anthropomorphic animals featuring as heavily into the series; they were present, but there wasn't much indication of their place in the world aside from what we're shown through the stories of Folken's two cat-girl cronies. But beastmen played a significant role in the movie, and it left me hungry for more information.
I also liked black-hat villain Folken. I liked the more ambiguous Folken from the series as well, but movie Folken found a place among some of my favourite villains. The conflicts of his character spring from very real places: quarrels over succession are classic and well documented and envy is something everyone struggles with. I did not like Dornkirk in the series, and setting up Folken in his place as the main villain really endeared it to me.
The characterization of some of the other characters is also better than I think others will give it credit for. I agree entirely that many faces seem to be in the movie for a cameo only, such as Milerna and Allen; again, their brief appearances left me wanting to know more about them and what their stories were. Hitomi and Van receive more attention and are richer for it. I can't argue with the point made initially that Hitomi's growth seems to come out of no where; but at the same time, the Hitomi we see through the first half of the movie is a character that many people can sympathize with, even in her extraordinary surroundings. We don't necessarily see the source of her conflict, but I think the writers are relying on us to see that this is a teenage girl who is disillusioned with life; its up to you to decide if that's enough.
Now, I've stood over this river and panned a few flecks of gold from the mud. The movie was a disappointment following such a great series, there's no question. But I took a few good things from it, and if I went and watched it again (its been several years) I am sure I could list a few more.