I don't really care about Katie Holmes or Rachel Dawes, just bring me Harvery Dent! I don't mean we should have Two-Face any time soon, but a strong Dent character (Edward Norton maybe? if they go for a bigger name) could have made Begins perfect. Building up a friendship and mutual admiration between Dent and Batman and see their ideals would made the turn into Two-Face a much more Darth Vader-like tragedy, which could be the main thread through two of three films.
But yeah, if we have to have a female character, Kate Winslet would fit. She did two of my fave movies last year, Eternal Sunshine and Finding Neverland. She would not just be a damsel in distress, looks alright against Bale and she's so much better than Katie Holmes.