I've beaten the game on Normal, selected Continue, turned the game on and off completely, and looked through all the options. I cannot find, nor have I been presented with an option to change skins. The only thing I've found is when I go to the challenge maps I can choose a different skin for Catwoman, but no option for Batman. This is really getting aggravating.
If you never downloaded any of the extra skins for Batman, they won't be available. Extra skins came with certain promotions or pre-orders of the game, and they all will be available to buy and download in the PSN store in December.