There wasn't much chemistry between Rachel Dawes and Bruce Wayne, either. I had a hard time really feeling the loss on either Bruce's or Harvey's part afterwards, I think, because of that.
My favorite scene of Maggie's was when she faced the Joker. And not out of some perverted "Oh, look, there's Heath holding the face of another Gyllenhaal" thing. But because the anger the character elicited in her brought out some real chemistry.
Chemistry is a funny thing. She had oodles of it with Will Ferrell, of all people. Never saw that one coming. But then, you have these two gorgeous leading man types, and zippo.
It's all about the pheremones, I tell you.