As far as the Joker goes:
-At the end of TDK he told Batman that they were destined to fight each other forever, if Nolan had even an inkling of an idea that he would have Bruce "retire" this should have been cut and it would have made a reference in TDKR easier because that chapter would have been closed where as the ending of TDK leaves it open.
-There really was not a need to reference the Joker in TDKR as it stands anyways. The whole city was against Batman and he was the one who stopped the Joker. The public was rallied behind Dent to reference the Joker one would have to reference Batman and that would not have been popular with the people of Gotham.
-If any reference was to be made it should have been done at the statue unveiling. Gordon should have pulled a Cain with some tears an recited a speech. The speech should not have mentioned the Joker by name. Instead, the speech should have gone something like, "He rid our city of fear, brought an end to organized crime, fought against anarchy and terrorism, took the fall for the sins of another, and ultimately sacrificed everything for the people of Gotham. He lived for this city and now we must live for him. He was a guardian, a protector, and (man tears) a friend". The reference to anarchy and terrorism would have sufficed for the Joker.
Just my thoughts.