Hush and the Black Mask need no changes.
Catwoman could be identical to her counterpart, but without the enhanced agility or anything.
Talia al Ghul would just be a simple assassin.
The Riddler would be a bomber that holds Gotham City at hostage. Near the scene of every bombing, he would leave a clue to his next target. Before actually becoming the Riddler, Edward Nygma would be a an obsessive-compulsive conspiracy theorist, and, in his research, discovers the truth behind the connection between the Arkham Outbreak, water poisoning, and destruction of the rails and the motive. However, after he comes public with his theory, the title "Ninjas Try to Destroy Gotham" is a bit of a stretch to most people, and is publically humiliated. Because of this, he attempts to take revenge on the people of Gotham City by blowing up key points the League of Assassins tried in Batman Begins. The only problem is that he would be more of a solo criminal, and since Batman 3 will have Two-Face, I don't think he'll be in any of the movies.
Firefly would be very close to his comic book counterpart, and would also be similar to the Riddler, but with more a penchant to arson than bombings. He also would not leave riddles to his target, and finding a motive for him would be pretty hard.
Hugo Strange would be good as Crane's replacement at Arkham.
Poison Ivy would be a radical environmentalist, and thus attack Gotham City for its polluting ways. She would be hard to adapt simply because of her motive is a bit...foolish.
Penguin, Killer Croc, and Great White Shark could be deformed freaks who attempt to take revenge on the people of Gotham for rejecting them. They and their army of "Freaks" would over-run Gotham the same way the Arkham inmates over-ran Gotham in Batman Begins. Great White Shark would be the head, with Penguin as his lieutenant and Killer Croc as his enforcer.
Characters like Clayface, Man-Bat, and Mr. Freeze would be next to impossible to adapt.