Well, I know that there is no way they can portray all of the characters in the film as the emaciated people of the animated series. Furthermore, I doubt:
a) That the audience will understand most of the film, provided its backstory is truly based on the animated series.
b) That Charlieze can really play the part of Aeon Flux, and not just wearing that black thong. The whole smart, badass, acrobatic, and deadly combination that made up the animated Aeon is not easy for most actresses to portray.
I too would much rather see the film in animated form. But, Peter Chung was a pretty eccentric animator/director/creater, kinda like Kubrick. Except that I doubt a studio would allow Chung full creativity in making a film. I know that the animated series got some cuts to it when it was aired on mtv..