The story line that General Petraeus is being forced to resign because the FBI uncovered an affair he was having with his former biographer is classic Washington DC theater. The story is a way of removing the politically popular General Petraeus from CIA without raising a political uproar. The real question is why?
This is just guess work, but I think there is a convergence of reasons for the newly elected administration to ease the General out. I think the administration does not particularly like the general and especially dislikes his political clout with congress. Also General Petraeus may have approved of some CIA operations or positions that have exacerbated the Benghazi tragedy and the administration does not want him before congress talking about this under oath. Finally Michael Vickers has developed a reputation based on nothing of being an intelligence wiz kid, yet he is politically harmless.
Michael Vickers is very highly thought of by the DOD civilian and military bureaucracy, primarily because he says little and does less. His SOF background (ten years experience from an enlisted man to a company grade officer) means he will probably continue to transform CIA into a para-military force. Although highly thought of by the congress, he does not have the political clout of Petraeus and so is not a threat. All this in the integrity free zone of Washington DC counts a lot more than the fact Vickers has only minimal experience actually doing intelligence and no experience at all in intelligence collection and analysis.
Phi Beta Iota: There are multiple signals in the open source literature about FBI Director Mueller being a modern version of J Edgar Hoover, with so much dirt on everyone that he can write his own ticket. Who, exactly, is proposed as the next Director of CIA will tell us more about qui bono? On balance, neither the FBI nor the DNI come out of this with clean hands. The latest report suggesting that Stephanie O'Sullivan–another member of the Jim Clapper harem — is a candidate to be D/CIA — is most troubling. If we were advising the President we would suggest that he fire Clapper, close down the DNI entirely, leave Morrell as Acting Director, and give Morell a new deputy for Community Management who would pick up the pieces. The idea of either Vickers or O'Sullivan as D/CIA is so abysmally lacking in integrity as to call into question the suitability of the DNI for anything other than forced final retirement. There is surely more to all this — although Patreaus has some pretty big warts in his background, all of these were known when he was nominated, so there is a strong element of betrayal in this story.