This game will probably be the most surprising, but Batman Begins is incredibly underrated. For reasons I can't comprehend, this movie tie-in wasn't well received when it came out but it had so many fantastic features. For example, you could intimidate you enemies, scaring them or taking them out 1 by 1, making the remaining goons more afraid of you, until the last guy sat crying in the corner.
You could also hide in the shadows, hang from wires, stealth attack and drive the batmobile. Importantly, Batman Begins perfectly captured the feeling of the movie, a fundamental necessity that most movie tie-ins fail to deliver. It's truly a shame the Arkham series never adopted the intimidation system from this game.