I think with a few strategically placed computer rips of old footage of Heath from TDK. They could have the Joker in the 3rd film, in a cell in Arkham. Possibly a way of bringing in a Harley Quinn type, ex psychologist becomes Joker fanatic, orchestrating the Joker's brand of chaos wjile he's locked up. You would still need a main baddie for the film though, and while I like Two Face coming back there are so many that could be used.
Dr. Hugo Strange
Killer Moth
Killer Croc
Deadshot
Hush
Mad Hatter
Ventriloquist
etc.
but I think the best story line would be the same one used in the John Byrne book the Untold Legend of the Batman from the early 80's, where Batman finds out his parents murder was actually a hit by mobster Lew Moxon.
Taken from Wikipedia:
Sometime prior to their murder, Dr. Thomas Wayne and his wife attend a costume party - to which Dr. Wayne wears a bat-like costume. Wayne is taken from the party, by gun-point, to meet racketeer and bank robber Lew Moxon. Moxon orders Dr. Wayne to remove a bullet from his shoulder. Wayne carries out the operation before overpowering Moxon and his men.
Moxon is arrested and sentenced to 10 years for armed robbery. As he is taken away he swears revenge on Thomas Wayne. Ten years later, a free Moxon informs Thomas Wayne that he will get someone else to extract that revenge (that someone being Joe Chill). It is suggested that Chill was told to leave young Bruce alive so as to provide an alibi for Moxon.
Years later Batman learns of Moxon's involvement in the murder of his parents, by which time Moxon is operating a Billboard blimp business. Batman's first attempt to convict Moxon for the murder of his parents fails, as Moxon is now suffering from amnesia and is able to pass a lie detector test. Batman determines that Moxon's blimp business must be a cover for illegal activities and continues to trail the gangster. Eventually, after uncovering Moxon's illegal activities, Batman confronts the criminal while wearing his father's costume (his own had been ripped during an earlier fight). On seeing Dr. Wayne's costume Moxon suddenly remembers what he had done. Thinking Batman was actually Thomas Wayne's ghost, Moxon panics and runs out into the street, where he is hit by a truck and killed.