A lot of people have seemed to have problems with Holmes, but I thought she fit in perfectly. Usually I see love stories in movies as useless padding, but I thought this one was fine.
(SPOILER)I thought the Scarecrow guy was great just because of the huge difference between him without the mask and him with it. He wasn't a guy you'd suspect of being the bad guy.
I loved Morgan Freeman's character, too. He fit in there and made it all the more believable. Was he added just for the movie, or was he ever in the comics?