Trivia: When Batman enters the clock tower, there's a flashback scene of Barbara being shot by the Joker. Before this occurs, go to the back wall and zoom in on the movie poster, "Dark Interlude." One of the names on the poster is Matthew Hagen. In "Batman: The Animated Series", Matthew Hagen was an actor who was transformed into the shape shifting villain Clayface.
Plot hole: In the DLC side mission In From The Cold there's emphasis put on Mr Freeze detonating the cryogenics generator he's been using in his research to take out militia tanks. Given they and almost all the icebergs explode it's amazing the Batmobile avoids instantly sinking into Gotham's waters.
Batman: I am vengeance. I am the night. I am Batman.
Question: Except for Two-Face, Killer Croc, Scarecrow and Jervis Tetch, why were the rest of the villains redesigned?
Answer: Probably because different people were working on the game. Scarecrow and Croc also have different looks if you've played Asylum, City, and Origins, they look different here too.
Rob245
Croc's redesign is easily explainable as it's revealed in this game that his mutation is accelerating.