These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
In Name Only: Pretty much the only things the film has in common with the animation are that the two main characters are an assassin named Aeon Flux and a scientist/dictator named Trevor Goodchild, and that cloning occurs.