The outcome of latest US crisis with Pakistan is still unclear. If Pakistan should effectively cease all cooperation with the US and ISAF in allowing transit through Pakistan, it would shut off a critical supply route in the winter, and one for which there is no good alternative. The Northern route is barely possible, but it would take months to find out just how much capacity is really available, and even under the best conditions, the capacity would be inadequate and the lead times would seriously affect both the campaign and aid efforts in 2012.
Pakistan needs US aid, however, and at least a minimal face of good relations with the US. It seems likely that this crisis will get papered over with a US/ISAF apology, a bribe in the form of better aid flows, and some kind of smokescreen about better liaisons. In the process, however, the US will face even less prospects that Pakistan will really crackdown on insurgent groups in the border area, or stop seeing Afghanistan as an area where it competes with India, and which is useful for strategic depth in some future war with India.
There will be a new façade, but the fundamental differences in strategic perspective will remain. A largely vacuous set of new pledges and promises in the coming conference in Bonn will not affect the reality that Pakistan now acts on the basis that the US and other ISAF forces allies will be gone at the end of 2014, and it must now serve its own interests in keeping ties to the Taliban, Haqqani, and Hekmatayer.
Like many other regional states - and many states outside the region - Pakistan will talk about new efforts at regional cooperation and helping Afghanistan, but it will seek to create a zone of influence along its borders. It will do what it can to use any talks between the Afghan government and the insurgents to its own advantage, and to try to push the Afghan government into closer ties to Pakistan and away from the US. It will try again to reach out to China as a substitute for US aid - although China is unlikely to be much more forthcoming than in the past. It will ensure that any remaining US advisory presence is narrowly constrained in ways that serve the Pakistani military, and place even more limits on US intelligence and use of UCAVs.
This will not cripple the US transition effort, but it will further undercut it. It will make reaching any kind of stable outcome in both Afghanistan and Pakistan as the US and ISAF withdraw their forces even more doubtful. It will also send a message to Russia, China, the Central Asian states, India, and Iran that they must do what they can to buffer themselves against the coming cuts in US and ISAF forces, spending in the region, and aid to Afghanistan and Pakistan. There will be more talk of a regional solution, aid pledges, and enduring support, but the reality will be very different. Every state will act to its own advantage and pursue its own view of its narrow self-interests.
This will make Afghanistan's "transition" even more difficult to do major without US and ISAF forces and anything like the present level of spending and aid even more difficult, and create even more problems for the US and its European allies in getting the legislative support and funds they need. It also will isolate Pakistan more, make the tensions between its civil government and military worse, and reduce outside aid. It will also mean that even if - as seems most likely - Pakistan does reopen its supply routes to the US and ISAF, relations will remain so tense that new incidents and crises in US and Pakistani relations are inevitable. This will undermine the already uncertain chances the US can actually achieve any stable benefits from the war after 2014 - either in Afghanistan or Pakistan
These issues, and the current state of the war and transition planning are addressed in a new CSIS report is entitled The Afghanistan War at the End of 2011 (pdf).