Originally Posted by The Joker
Unless there's an Arkham breakout, there's no problem story wise with Joker being absent.
I think that's why they use Blackgate in this movie as the breakout instead of Arkham like they did in Knightfall. I would suspect if Ledger was still alive we would have seen a bit of Scarecrow/Joker team up with them kidnapping the mayor.
But I truly hope they mention him.