You'll have to bear with me, it's been a long time since I've watched this series, and I was rather young when I did. Unfortunately for me, this series was not meant for children. Anyway, I can recall a few specific things:
It was something about two cities, at war with each other I believe, and a female main character who was caught in the middle. I remember an incredibly corny villain who did something sinister, laughed evilly, then promptly folded his legs and fired rockets from them to escape into the air. I remember laughing, because even then, I wasn't too young to recognize something cheesy. It's possible that my lack of memory has me combining different characters, but if so, I probably laughed at them all, anyway.
I also recall a climactic scene in which either the main character or some acquaintance of hers...I don't think I knew the difference anyway...had her legs severed above the knees by an energy field, but instead of bleeding wounds, guts, or even a well-aimed camera angle, you could clearly see her thighs ending in solid red circles. Perhaps she was actually a minion of personified red licorice. I wouldn't put it past the show's writers.
I used to watch this show at a friend's house, and we thought we were being rebels by turning it on. Now, I see stills of the characters' faces, and I am reminded of how I didn't really understand or enjoy the show, and why I looked forward to watching Max (I believe that was the name, anyway), an animation about some guy who turned into a hulking monster, which came on after Aeon Flux was over. Nowadays, of course, nobody seems to recall either of the two. Perhaps it's better that way.
Oh, and the half-star in my rating is kind of a glimmer of hope, that maybe there was some depth to Aeon Flux that I simply missed as a result of my being about twelve years old at the time. But I don't plan on watching it again to find out.
(Post-edit: I've lowered my critique to one star. This is because I just gave Titan A.E. one and a half. If you had to choose between the two, for your own sake, PLEASE watch Titan A.E. before you watch Aeon Flux.)