Neither of them were that great, but I agree with others that it would have been better if Gyllenhaal was in BB to begin with.
Holmes always looked awkward in BB, especially in scenes where she's trying to escape from danger (awkwardly hitting that mobster with her purse, tazing Crane). I just never bought into that friend/relationship, especially in the final scene in front of the ruined Wayne Manor.
If nothing else, Gyllenhaal looked a bit more mature and self-assured in the role, like she wasn't being written as a young woman who was in way over her head. And at the very least, I still remember the rooftop terrace "Don't make me choose" conversation in TDK, so she has that going for her. That said, she was still stilted and wooden in parts, and barely made any impact in the film whatsoever.