Well, the movie is quite different. The way I saw it, it went for visual style, first and foremost, then it tried to implement a coherent storyline that would make sense. The trouble is that the film tried to tell the story so it would have a beginning, middle and end in a classical way but I felt that there wasn't enough time for all that. Plus, as you yourself observed, Aeon Flux doesn't lend itself for this kind of storytelling approach. It deliberately puts you into the middle of something you don't know the beginning of and most likely will not know the end of either. I'm not going to go into the story itself as one should really look at the movie as a totally separate entity from the animated series (although it is helpful to be aquainted with the stories from the series as certain elements are also used in the movie).
However, the film looks really good and Ms. Theron is very appealing
and did a lot of great work (as she does) but still couldn't change the overall feeling that the original charm and charisma of the characters has been altered to fit a particular level of conformity. In other words, both Aeon and Trevor were made into likeable characters or heroes without ambiguity whereas I think it's that very ambiguity in Aeon's and Trevor's original character that appealed (to me) in the first place.
For me, the animated Aeon Flux is really a series that explores the actions of characters who have their traits and idiosynchracies and all that in a fantastic world. Those explorations often go into the abstract realm and definitely may not always make sense. But that's the case with a lot of art. Peter Chung said himself that he doesn't want to interpret Aeon Flux because he wants the viewer to take away whatever they feel like. Having watched the series again recently my brain was certainly tickled in different ways than years back
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