As you will have noticed, an article in the Rolling Stone has meant the end of the career of general McChrystal as head of the US military in Afghanistan. The main reason was that he was openly critical of Obama in front of a journalist. That is a major mistake for a soldier.
However, the main message of the article is that the military has lost the hope that it can win the Afghan war and in many ways that is more interesting. Given that this happens so shortly after a major troop surge this doesn't bode well.
McChrystal is partly responsible. He was great as a Special Operations commander in Iraq who shot and captured insurgents. But in Afghanistan he needs also to "win hearts and minds" and in that part of guerrilla fighting he has proved to be a failure: immediately after he started the number of civilian casualties started to skyrocket and when protests finally forced McChrystal to intervene he did it with such a rigorous restriction-of-force instruction that the US soldiers now feel seriously handicapped. Fighting a guerrilla war requires also considerable effort from the civilian side. But McChrystal has only contempt for any civilian who isn't doing his bidding and has even taken over tasks that should go to the top US diplomat in Afghanistan.
Petraeus may well turn out similarly problematic. Just as McChrystal he made his name in Iraq and he knows little about Afghanistan. It looks like Obama has again chosen the assurance of a big name above real expertise. This protects him from immediate criticism but me be problematic in the long run.
Petraeus role in Iraq was that of the cynical turn-around manager. He was prepared to shut the whole operation down but was lucky to find that in its arrogance the US military had left some major opportunities for improvement unused. But such easy opportunities for improvement seem missing in Afghanistan. The only thing that could help is building good relations with local people so that the US military gets better intelligence and cooperation and becomes less dependent on Karzai.
The question is whether Petraeus will be capable to achieve that. It might have been a much better choice to select some lower level US commander who in his province in Afghanistan has shown that he can do that.
In times of peace the promotion of officers in the army often happens on grounds that have little to do with competence. This is because in times of peace it is difficult to determine who is performing well. So seniority and having the right contacts are often more important. In times of war however, performance is very visible and promotions go very different. Some people may see their career advance very fast. But on the other hand there is much less reluctance to push aside those who don't perform. It is time that Obama shows a bit of this war mentality.
And then there is the political/diplomatic side. Here the US has seriously handicapped itself in Afghanistan. While in Iraq the US ambassador forms a rather effective duo with the military commander, in Afghanistan the diplomatic role is dispersed. You have the US ambassadors in Afghanistan and Pakistan and "special envoy" Holbrooke. You have the ISAF commander (a Brit). And to top it of McChrystal had acquired some diplomatic role for himself too.
As I have written before, Pakistan desires a poor and backward Afghanistan so that its own Pashtu's won't feel a desire for separatism. I see no easy solution for that. But ignoring the massive support that Pakistan is giving the Taliban is ignoring reality and that leads nowhere.
In my opinion the main goal of the US should be decentralization. Karzai may not like it, but that is the way Afghanistan has been ruled for centuries.