I read about how they had a few cuts of the film, including one that just went in chronological order with all the scenes. The one we got was the "dossier cut" where they laid out the cast in a sit down meeting, paging through who's who. I thought this worked the best, as it easily introduced us to the characters and had the flashbacks make sense.
The Joker scene at the club was a little weird, but I loved the ACE Chemicals scene where Joker had Harley dive into the tank. That bit where he walks off and is torn between "fuck it, she'll die and I'm free of her" and "she's so crazy, she'll do anything for me, I should save her" was cool, and the image of him diving off with his gun holster swinging out was great. The music fit well too.
I do think with a great writer, they could do an awesome Batman/Joker movie. Thankfully, I heard that the upcoming Batman will have multiple villains. So we might get Joker, but it won't just be Joker - which is something people have complained about. Though, The Dark Knight, which was a Joker movie, also had Two Face, Scarecrow and Sal Maroni. So it is possible to have a Joker story but also highlight other villains. I'm hoping for a The Long Halloween sort of story. Or, it would be awesome to have a Batman movie set during Halloween. Batman Returns was set during Christmas.