I'm sure we can rule out Hugo Strange as TDKR villain now since he's in Arkham City. It's published by Warner Bros and Eidos so I can't see WB, or even Nolan, wanting the biggest film of 2012 to have the same villain of a 2011 video game.
Plus the fact that Arkham Asylum was a very well received game by critics which then led to increased sales which then has, undoubtedly, created much anticipation for the new game.