I'd replace the entire Holiday-killer subplot with Joker causing havoc in the city--robbing banks, homicide, etc. Harvey tries to prosecute him but he gets acid in the face. I know a lot of people don't want Joker scarring Dent, but that's how I want to see it, and how it was in the first draft of the script anyway.
IMO, it would be one of those instances where its a great departure from the comics (just like Ra's training Bruce, Crane running Arkham). It just feels right. Joker's crazy, he has an acid squirting flower. It just works.