ISAF has done a great job in working to secure Afghanistan however Pakistan has a vested interest in keeping the Taliban, Haqqani Network, and Hezb e Islami active and vital. The reason for this Pakistan wants to either have direct control or see a destabilized Afghanistan as that helps gives them strategic depth against India. The three groups I just listed have had and still do harbor and train other Pakistani and international terrorists with Pakistan's tacit approval and in some cases material support. The good Taliban as the Pakistanis see these groups are a strategic asset and will not move against them. Our drone strikes against the the Haqqanis are mere pin pricks and since we cannot hit Quetta where Mullah Omar's Taliban reside we cannot hit their command structure either.
Remember Pakistan's Tribal Area is the key.