Breaking Up Is Not Hard to Do - Why the U.S.-Pakistani Alliance Isn't Worth the Trouble, by Husain Haqqani. Foreign Affairs, March/April 2013.
With the United States and Pakistan at a dead end, the two countries need to explore ways to structure a nonallied relationship. They had a taste of this in 2011 and 2012, when Pakistan shut down transit lines in response to a NATO drone strike on the Afghan-Pakistani border that killed 24 Pakistani soldiers. But this failed to hurt the U.S. war effort; the United States quickly found that it could rely on other routes into Afghanistan. Doing so was more costly, but the United States' flexibility demonstrated to Islamabad that its help is not as indispensable to Washington as it once assumed. That realization should be at the core of a new relationship. The United States should be unambiguous in defining its interests and then acting on them without worrying excessively about the reaction in Islamabad.

The new coolness between the two countries will eventually provoke a reckoning. The United States will continue to do what it feels it has to do in the region for its own security, such as pressing ahead with drone strikes on terrorist suspects. These will raise hackles in Islamabad and Rawalpindi, where the Pakistani military leadership is based. Pakistani military leaders might make noise about shooting down U.S. drones, but they will think long and hard before actually doing so, in light of the potential escalation of hostilities that could follow. Given its weak hand (which will grow even weaker as U.S. military aid dries up), Pakistan will probably refrain from directly confronting the United States.
A provocative article from Pakistan's former Ambassador to the US. Some context about the author:

Commentary: Geopolitical conundrum, by Arnaud de Borchgrave. UPI.com, Feb. 22, 2013.