The Pakistan "security establishment" (the Pakistan Army, ISI) is sometimes thought of as a Frankenstein monster in the US. The US is sometimes thought of as the great Satan in Pakistan & the rest of the Muslim world. Both thoughts are very far off from the truth. The truth is that when the US Pakistan interests were aligned in the 80s, the Pakistani security establishment worked very well with the US with very little problems. Today however, the US's geopolitical/strategic interests are not aligned with Pakistan's national integrity/security interests. Which is why there is "friction" between the US & Pakistan's security establishment.
US troops might have left Iraq, but a country that did not suffer from sectarian violence pre-2003 & did not have any Al-Qaeda has become a hotbed for Al-Qaeda extremism today. The rise of the AQAP in the Middle East, the Al-Shabaab & AQIM in North Africa leaves a mark, & a signal for future foreign intervention (for influence) in the region. Likewise, the US is trying to plant its seeds in Afghanistan, to do its bidding once it withdraws it troops, regardless of whether that is the Taliban, Karzai or anyone else. This is where the US is facing difficulties, as it is facing a formidable adversary in the form of the Pakistani security establishment.
US Senate & Congressional hearings openly discuss "empowering" the Pakistani civil society as a counterweight to the Pakistan security establishment, to wane its influence. Dubious leaks, dubious reports from unnamed officials, "military-civil society clashes" show that the US will go out of its way, & will take all the painful & time-consuming strategies that can help it achieve its goals: to weaken the Pakistani security establishment. There is a popular notion in the West that the Pakistani security establishment is the reason for the weak civilian government. They think that empowering the civil society can help weaken the security establishment. Time will tell whether that is the case or not.
There is an interesting mindset in the West that the Pakistani security establishment is "inherently evil", is the bane for the region, does not support peace, & the reason for all the troubles in the region. The Pakistan security establishment is concerned with safeguarding Pakistan's national integrity/security interests, & every other thing is secondary. The fact of the matter is that the Pakistani security establishment will support anyone, will do anything to safeguard its national integrity/security interests. Pakistan's concerns with Afghanistan or India are in relation with its national integrity/security interests. Pakistan, unlike the US is not a nation that aspires strategic geopolitical interests/influence, everything it does is in relation to its national integrity/security interests. The Pakistan security establishment will not favor anyone that goes against them.
Some people think that the Pakistani security establishment is fixated on India. Cross border violence into J&K has gone to an all-time low; the insurgency from the Maoists & in the North East have taken the front seat, & Kashmir has taken the back seat. Musharraf, & his successor have both showed willingness to resolve Kashmir amicably with India, the major thorn in Pakistan-India relations. If that is amicably resolved, the US will find it very hard to play as a spoiler in the region (to advance its geopolitical strategic interests). The Pakistan "resorting" to China (moving away from the US) helps the US use India as a counterweight to China. The interesting thing to note here is that while China, India, Pakistan have genuine national integrity/security issues/interests with one another; the US mainly has its geopolitical strategic influence interests (not any real national integrity/security issues) in the region. Which is why it is acting as a spoiler in the region.
Contrary to the belief of some people, Pakistan will not be left isolated by the US post 2014. Pakistan's geographical realities show it is too strategically & geopolitically important for the US to isolate. The isolation of the Pakistani nation will only make them take China's cradle, & will reduce the US's geopolitical strategic influence in the region. Hence, the US strategy is not to isolate Pakistan post 2014, but to isolate the elements of Pakistan (Pakistan security establishment) that are acting as obstacles to the US advancing its geopolitical strategic interests in the region. Pakistan's diverse ethnic makeup/realities show that Pakistan will not fall under the control of extremists either.