Because of the removal of key Al Qaeda leadership from the battlefield in Afghansitand, Pakistan and elsewhere, the group has become more decentralized. (http://www.thedailybeast.com/articles/2009/10/16/the-taliban-al-qaeda-connection.html) Some have claimed that this has made Al Qaeda more dangerous and more difficult to track. This may be true, but at the same time they are also less capable of planning and executing as complex of operations as 9/11 since they are now more scattered and a significant amount of their key leaders have been killed or captured. They have however become more difficult to track as they move into new territories such as Yemen where there is less intelligence on their activities.
In the future it is possible and even likely that the US could conduct peace talks or reach a compromise with the Taliban granted they made an agreement to not to indirectly sponsor terrorist attacks by hosting groups such as Al Qaeda within their borders. Similar peace talks would be nearly impossible with Al Qaeda because of their stated goal of a global Islamic state.
Will the recent killing of bin Laden change the future relationship between al Qaeda and the Taliban? It is likely that it will change, although not diminish. The al Qaeda and Taliban relationship was largely based off of the personal relationships of Haquani and bin Laden. So into the future they will likely continue to work with each other due to their long common history and some shared goals but the relationship may change due two these two key leaders within their organizations being removed.
Barfield, Thomas J. Afghanistan: A Cultural and Political History. Princeton: Princeton UP, 2010. Print.
Crews, Robert D., and Amin Tarzi. The Taliban and the Crisis of Afghanistan. Cambridge, MA: Harvard UP, 2008. Print.
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