I prefer the AA costume to be honest. Though I'm sure Rocksteady made the choice for a reason. I think its to do with her behavior. I mean this is what is stated on her profile on AC website: "Ms. Quinn's behavior has become evermore erratic and vicious".
Not to mention that in the gameplay trailer she says "It would be a shame to get blood all down my nice new outfit" She's going to be tougher.. Most likely because she has to protect the Joker.
I'm sure it will make more sense as time goes by :)