IMO, the Joker is supposed to be dark. "Hello, we're bad guys." lol. I didn't think he was any darker than Heath's, in fact Heath's felt a bit more "real" in his darkness. The Nicholson was in the dry, deadpan crazy comments IMO, not in the portrayal. Nicholson had the best mix between funny and psycho IMO. "Where does he get all those wonderful toys?"
I haven't seen the final film, so I don't know what they changed. Sounded like not much. The antagonists were the real let down, but the motivation of the squad was also a big WTH. Even with the "control" method, it didn't feel realistic.