I think the big problem was that Bush permitted Iraq and Afghanistan to enshrine Islam in their constitution - at a time when we controlled them and could have removed that from their proposed constitutions. Had he gone for a secular state, it might have worked, or at any rate, better than it has.
It is questionable that one can install a US type of government in a Middle Eastern country, which is fixated on the Great Leader. But permitting Islam to be part of it in an official way killed the whole concept from the start.
The problem with Bush in this respect was the same problem that he had with everything he did: he bent over backwards to show how “fair” he was and prove that he was not biased in favor of Christianity or capitalism or anything else that the Democratic party considered evil. So in a sense, I see his big error in the Middle East as basically the same as his big errors in US government: being too intimidated by the opposition party and too desirous of proving his “fairness” to actually stake out any positions of his own.
As for Obama, the secret is simply that he’s hostile to Christianity and does everything possible, both domestically and in foreign policy, to make life difficult for Christians.
The big problem is that the US has rejected Christianity. The plight of the ME Christians is just a ripple effect.