I never liked Scarecrow and that's really my only reasoning for not liking the villain choice. I understand it from the plot perspective, he's just starting out he needs a villain that's sane and not too powerful. Using Ras definitely made this tollerable for me.
The casting aside from Bale was wonderful. Bale doesn't have the power in his voice that Batman should have. It just sounds like he's a heavy smoker when he's in that persona. As for him as Wayne, I didn't like how he acted in public. I felt like he acted too much like his alter ego and too intelligent. I've always preferred the writing of Wayne as the playboy with no knowledge in the business world; it seems more realistic as a cover to me. He also lacks the necessary jawline for Batman.
More than anything, though, I hated what they did to the Batmobile and the pathetic look of the batarangs.
That said, I can't wait for Dark Knight. The Joker is my favorite villain of all time, and it looks like Ledger didn't fuck it up too much. I hate that they gave him a glassgow smile as the makeup though; they made him look more like a junky than a psychotic, evil, son of a bitch.