Gotham become more effed up once Batman came to the scene.
Our very strength incites challenge. Challenge Incites Conflict. And Conflict Breeds Catastrophe - Vision, Civil war.
Jim Gordon is an honest cop/detective at the time (i think) then became commissioner when batman came to the scene.
Corruption is deeply ingrained in Gotham, with all the gangs controlling for power in the city, even in the police.