What is most plausible is the CIA and government intel where simply caught by surprise and failed to properly react. Nobody wants to believe our intel community could be this incompetent so we are taking this simple explanation as implausible, when logically it is the only version of events that makes any logical sense.
Furthermore, Petraeus is an honorable military officer, he would not resign his post over an intel kerfluffle. Nobody asked him to resign or challenged him to resign. His resignation is purely based on getting caught with his pants down, a direct violation of his own personal honor code.