Jeffrey Goldberg and Marc Ambinder have an expose on Pakistan's nuclear program. Money quote:
The Pakistani government is willing to make its nuclear weapons more vulnerable to theft by jihadists simply to hide them from the United States, the country that funds much of its military budget.
Goldberg flags a subsequent report that Pakistan is increasing security on its nuclear weapons. Eli Lake fits Ambinder and Goldberg's article into a broader pattern of evidence suggesting "Pakistan’s national security establishment is at war with the United States, while its elected leaders are putative U.S. allies." C. Christine Fair goes further [pdf]:
Ten years into the most recent engagement, in the wake of the 9/11 attacks, it has again become abundantly clear that Pakistan’s strategic interests diverge starkly from those of the United States. Most observers of the U.S.-Pakistan relationship admit that Pakistan’s allies—such as the Haqqani Network, the Afghan Taliban and Islamist militant groups such as Lashkar-e-Taiba, among others—are America’s foes. It is equally clear that America’s ascendant ally in the region—India—is Pakistan’s nemesis. Thus what bedevils U.S.-Pakistan relations is not pervasive distrust but rather a surplus of certitude: certitude that, for the foreseeable future, U.S. and Pakistani strategic interests have only a small—and quickly vanishing—area of overlap.
Spencer Ackerman reacts by getting angry about America's relationship with Pakistan. Amitai Etzioni is pessimistic that Pakistan can be part of the solution in leaving behind a semi-stable Afghanistan.