I just finished watching this film. I was pleasantly surprised because I actually enjoyed it. There was more to it than watching Chalize Theron romping about. And the fact Marton Csokas was in it didn't hurt either.
I've never seen the Aeon Flux graphic - I hesitate to call it a cartoon even though that is what it was - but I did know of it. Since I can't compare the two, I don't know whether that lack had any effect on my perception of the film. Because I enjoyed it, I'm going out on a limb and say it didn't have any effect whatsoever.
The movie is definitely worth the price of a rental in my view.