They left the character in for good reasons, I'm sure. And to those who say "batman shouldn't have a recurring love interest" in the comics, there were severa instances where Bruce Wayne had what could be almost descripbed as a serious relationship, one of these leading to the storyline where the woman was killed and Bruce Wayne was the lead suspect, and he didn't know if he did it or not (at the time, he was having problems with the whole bruce wayne/batman thing, going a little crazy, to say the least)
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I think the first Batman and Nicholson as Joker were the best of the series before Batman Begins... but they were still very comic like. Batman Begins is a more serious, sinister, series, and Nicholson as Joker would just make it too comic-like."
This is ironic, because Tim Burton hates comic books, and did everything he could to thumb his nose at comic book continuity with his two Batman movies. Batman Begins is MUCH more like the comic books than any batman movie that has ever been made.