Since I'm on a leave of absence I don't have access to the Rolling stone article about Afghan campaign top general Stanley McChrystal, but here's a link to a piece with some key excerpts. His comments look to fit the classic Washington definition of a gaffe: an inadvertent or inconvenient dollop of truth, the eternal enemy of all things governmental.
I'm convinced, for example, that McChrystal's characterization of Obama as ill-informed and somewhat disengaged about Afghanistan is almost certainly true. Obama had no background in or interest in foreign affairs before being elected, and his decision to call Afghanistan the "right" war was strictly political, to countermand the impression that he is a war wimp. He seems to have no clue just how complicated Afghanistan is -- or how unnecessary it is for the U.S. to fight there, given that the Taliban is an indigenous Afghan movement and al-Qaida, which does have international ambitions (though little operational capacity) has no real foothold in Afghanistan. The fact the al-Qaida and the Taliban are different outfits that don't have identical agendas seems to have escaped him.
While McChrystal's slams at the administration (except for Hillary) ring true, however, his own plan is deeply flawed and rife with wishful thinking. Classic counterinsurgency doctrine depends on a stable government with a reasonable amount of popular support and effective security forces to succeed. This is hardly the case in Afghanistan, where Karzai's rule doesn't extend beyond Kabul and the government (and Karzai's brother) are profoundly corrupt and unpopular. Not only is it unnecessary for the U.S. to dictate the political outcome in Afghanistan, it is most unlikely to succeed in a country with deepseated suspicion of outside powers and no desire to have an effective central government. So there are no good guys in this flap.