Origins had the best story of the series. The Joker reveal was groanworthy initially, but it justified itself and even redeemed itself in the context of the story it was telling. Bruce had an actual arc and the game made attempts to make its characters interesting and likeable.
People just don't like it because it was a reskinned City--WHICH PEOPLE HAIL, BY THE WAY, so I don't get how having that same gameplay somehow makes the game worse by comparison. Introducing the crime scene recreation/detective bits were awesome and actually made the Batman fantasy more fulfilling than literally just beating everyone up.
Best story, best art direction, best atmosphere.