I would say that, in general, I like the art style, mainly the character models, more in Origins. For most of the characters, it is sort of a tie (e.g. Joker), but specifically for Batman, Deadshot, and Bane, I think Origins looks much better.
Bane (Asylum): http://tctechcrunch2011.files.wordpress.com/2009/04/bane-big.jpg
Bane (Origins): http://img.gawkerassets.com/img/18vi7r09uwly9jpg/ku-xlarge.jpg
For Batman, I guess I never really had any other games to compare to at the time, but Asylum/City Batman's face just looks.. off to me. It may have to do with the cowl though. The ears are much too long imo. However, the same suit looks much better in this image (although this isn't a screenshot): http://static1.wikia.nocookie.net/__cb20110610104753/batman/images/7/79/Batman-arkham-asylum-artwork-batman.jpg
For Bane, the Asylum/City one just looked comically large (I know it is comic-book based game, but still). Even ignoring that, the tubes being all of the place just looks funky.
For Killer Croc, I actually prefer how he looks in Asylum/City, he doesn't look nearly as menacing in Origins and, looking at his character profile, he looks sorta-kinda like a krogan from Mass Effect.