I wouldn't consider Ennis' god in Preacher to be the main villain. It was his ineptitude and arrogance that lead to a lot of the problems, but he wasn't really someone that the protagonists need to beat. I think the main villain for that series was the system (be it the hosts' or the people's.)
Contrast it with Cliver Barker's Next Testament, where the god of colors (god the father/old testament god, there's actually three of them there, with the other two hinted at as the holy ghost and the son, who were responsible for imprisoning the god of colors) was clearly portrayed as malevolent and capable of genocide just for shits and giggles.
