Heath Ledger's Joker is an extremely strong character IMHO. You rarely see a villain as nihilistic and outright evil, and as chaotic as him.
I can completely understand that. The Joker as portrayed by Heath Ledger does have some strong traits. He's one of the few openly Neutral Evil characters in film. I think you misunderstand if you think he's chaotic. In Chaotic Evil, there is an attitude of, "The only way to get ahead is on the backs of others." But there is no sign that his Joker character is trying to advance himself or even his own survival as an agenda - "He just wants to watch the world burn." Destruction for its own sake, often motivated because you don't believe the world is worth saving, is a neutral evil agenda.
And while the Joker as neutral evil in motivation is something I'd accept, the fact is that this character, while strong isn't what I want to see in The Joker. That makes it difficult for me to relate in the way someone with no prior experience of the character probably would. Ironically, by removing his charm, his humor, they make the joker less menacing because the really disturbing thing about the character is his charisma. We want our pure evil to look ugly, scarred, and venomous so that we can easily reject it. When that same pure evil is presented as an anti-villain, it's disturbing. This is particularly effective when you hide the evil at first, garner some empathy, and then just rub it in the person's face that the villain has no redeeming qualities at all.
His motives are hard to fathom, it's next to impossible to foresee his next move. The makeup alone tells you that he is approaching hi sunset, just making the character all the more interesting. What is his history, what has made him like this? He was a successfull criminal, but how so?
What you see as strengths, I across the board see as weaknesses. If his motives are hard to fathom, then the character hasn't been drawn well. The reason his moves are impossible to foresee, is that the character possesses profound 'magic' - the ability to conjure and teleport bombs. He seems to have no logistic trail at all. Things just happen magically because he wants them to. He has no history. He has no backstory. He has no actual means of being a successful criminal. There is no reason to think this guy could organize or create or stay in charge of an organization of the size that would be required to pull of his outlandishly complicated schemes. He's not at all a believable character, and his schemes happen with the power of plot. There is no way for a detective to anticipate him because there is no reality behind what he's doing. It's like watching the story told by a bad improvisational DM where things just happen to challenge the PC's. It's not like there is any story behind what we are watching on the screen. It's shallow and empty.
Christian Bale's Batman isn't as strong a character...
Not only is his batman completely unsympathetic and flat, so that we are never really rooting for him, but he's just not given enough time to develop the character. The story wants so much to happen in 2 hours, that by the time we jumped through all the stupid hoops necessary to advance the plot points, exposition to tell us what is going on, and minor character introductions - there just isn't any time to develop Batman. Nolan is relying on the fact that Batman is pretty darn iconic to begin with and that people are going to bring some notion of the character and that he's someone you should care about to the film.