That sort of ad hoc pseudo-policy is to be expected from people whose criteria to team-building is and was completely political. They were clearly much more concerned with loyalty and ideological compatibility than anything resembling, say, knowledge and expertise. So no surprise that things have turned out this way.
Couple things, though, regarding Turkey and Pakistan specifically. Turkey has been given a pass on its ethnic cleansing of its own Kurds for years, to the point where we even sold them the artillery with which they decimated thousands of villages and killed tens of thousands of people. They have suddenly gotten pissy and more brazen with the misbegotten attempt at drafting a resolution condemning the Armenian genocide. Many things are the fault of Bush's incompetent handling; this specific episode is actually not one of them.
Even without screwing our national interests for more of this non-binding resolution bullshit, the problems with Turkey run much deeper. The Dummycrats who pushed this thing through simply gave the Turks handy pretext. And if Turkey, which has been humping everyone's legs for EU membership for years now, still harbors any hope at all of getting in within the next generation, they'll stop for a moment and think seriously about thier next move.
As for Pakistan, it's pretty much out of our hands, and has been since day one. All we can do is what we've been doing, which is give Musharraf more money to work with, and stay out of his way as much as possible. But the people who have been causing problems there ignored the Durand Line long before Musharraf, and will continue to do so. And bringing back a corrupt door-stop like Benazir Bhutto solves nothing.
Obviously the biggest mistake here was invading Iraq. But most of us agree that invading Afghanistan was entirely justifiable, and even had we stayed and committed the necessary troops and done everything we needed to do, it would have become even more of a flashpoint for the crazy bastards in the region whose hobby is inflaming these tensions. So it seems Pakistan was going to be a huge problem any which way it was handled; perhaps we should simply be grateful that these inept tools largely kept their mitts off it. Whatever his faults, Musharraf appears to be far and away the best of a lot of bad options.
At the risk of overstating the painfully obvious, none of the options in the region are good. Even if it were economically possible to totally disengage from the region overnight, then what? Geopolitics, like it or not, has never favored power vacuums. You are left either with squabbling states jockeying for regional position, an acceleration of the hollowing-out of Iraq and Afghanistan by the sectarian gangs posing very real threats to their respective central governments, or most likely, the great powers of the region -- Russia and China -- swoop in and offer to "help".
Again, this administration's predictable incompetence and venality certainly compounded the mess, perhaps irretrievably. But there was never a cut-and-dried solution or even recommendations; if Cole offers any I missed them. Maybe these are simply the natural questions of an overextended empire, of a society that refuses to even consider living within its means and consuming at a more realistic rate.
Turkey is a country that frets constantly and violently over its official legitimacy, and is facing increasing internal and external pressure. We have never done anything about that except make sure that we could make a buck. Pakistan has always been a country that, even in the best of circumstances, is problematic because of its mutual hostility with India. There's no doubt that the Cheney administration, in its evangelical zeal, could find a way to fuck up a baked potato, as the saying goes. But neither country was exactly a bed of roses during the Clinton years, nor were they going to be after the Cheneyites have toddled off to the conservatard rubber-chicken circuit.
Since Cole actually does have profound knowledge of the region and people in question, it might be more helpful if he simply proposed some ideas that he thought could work, and get the discussion going from there. Even Bush's supporters know that he's screwed the pooch royally; the question even before 9/11 was always how to bring large societies of virulent traditionalists along without exploiting their resources and discarding them and needlessly enraging them.