And instead of concentrating so much of the U.S. military effort in southern Afghanistan, particularly in sparsely populated Helmand province where a disproportionate number of Marines were deployed, Karzai wanted resources directed at the eastern districts of Afghanistan that are key to Kabul’s security. These areas were neglected by the widely-touted Obama troop surge in 2009 and, as a consequence, the security situation in the east has increasingly become more precarious (see here and here). Indeed, just days after the Kerry-Karzai understanding was announced, the governor of Logar province, located just south of the capital, was assassinated.

Writing in the current issue of Foreign Affairs, Ambassador Eikenberry – who had earlier served as the top NATO commander in Afghanistan from 2005-2007 – acknowledges that the key premises undergirding the COIN strategy were “spectacularly incorrect.” He concedes that U.S. officials were remiss in not taking more seriously Karzai’s consistent point that the insurgency they diagnosed as basically an indigenous phenomenon was actually “mostly a ‘Made in Pakistan’ product that Islamabad was forcefully exporting across the border.” He notes that:

“Karzai disagreed intellectually, politically, and viscerally with the key pillars of the COIN campaign. The result was that while American military commanders tirelessly worked to persuade the Afghan president through factual presentation, deference, and occasional humor that the plan was working, they never seemed to consider that Karzai just might not be on board.”

Nor, it should be added, did civilian leaders in Washington ever pause to consider whether Karzai’s tantrums could be linked to their own management of the war or to the confusing signals they sent on strategy. The dissents that Vice President Joe Biden made internally about the COIN effort have been allowed to seep out, particularly his contention that the Taliban insurgents waging war against Karzai’s regime were not really America’s concern. And Biden’s remarks during his debate last fall with Paul Ryan – “We are leaving [Afghanistan] in 2014, period” – were so emphatic that they seemed to undercut the administration’s professions about it long-term commitment to Kabul. As Stephen Biddle and Michael O’Hanlon observe, this kind of mixed messaging from Washington has “interacted with Karzai’s various shortcomings to create an ever more difficult relationship.”

Many of the snags in negotiating the bilateral security agreement were due to these protracted quarrels over strategy. Kabul had insisted that the U.S. promise, first, to undertake military operations only in conjunction with Afghan forces and, second, to guarantee the country’s external security. Washington had feared that the latter demand would only deepen its embroilment with Pakistan, though both issues have reportedly been finessed in the deal now reached between Kerry and Karzai.

One goes to war with the allies one has, to appropriate a now-famous Washington aphorism. And in truth, the disputatious Karzai has unnecessarily complicated the U.S. effort in Afghanistan. But the Obama administration’s own derelictions have also contributed much to the testiness. The White House would be wise to absorb this lesson as the endgame in that country approaches.

David J. Karl is president of the Asia Strategy Initiative, an analysis and advisory firm. He blogs on U.S. foreign policy at Monsters Abroad.