It's hard to imagine what they were thinking with this one. I watched some of the original animated shorts a while back, just after they released them on DVD. In its original television form, Aeon Flux was bizarre, perversely sexual, and incredibly (almost pointlessly) violent--an utterly-incoherent throwback to Heavy Metal's drugged out wanderings.
So how do you turn that kind of visual candy into a live-action film? Apparently, you don't try. You write a pastiche of future-dystopia, throw in a set of visual non-sequitors, and cast Charlize Theron--who is a fine actress, but simply can't summon the kind of gaunt, sardonic brutality that the role requires. Director Karyn Kusama likewise tries her best, but can't direct an action sequence worth watching. Perhaps this kind of thing is really best done on the cheap nowadays--fans of Equilibrium who watched Kurt Wimmer's disastrous Ultraviolet will note the similar feel of Aeon Flux's panoramic scenery and expansive color palette, which (oddly) rob the gunfights of their impact.
I respect the attempt to turn such a weird little property into something that MTV could license for Burger King soda cups, but let's be honest: it never had a chance of being a good mainstream movie. The only way it could have been great would have been to embrace the genuine weirdness of its inspiration--become something like Naked Lunch with guns and S&M couture outfits. Even then, it probably would have been terrible--the show doesn't honestly hold up well today, particularly in extended viewing sessions--but it would have been a lot more interesting.