The political leadership, Federal and Provincial, does take much of the blame (in the present) in that they have not formulated and implemented effective counter-terrorism policies. There is a need for the FIA and IB to be made autonomous (appoint the DG's through a balanced parliamentary committee) and for significant expansion and capacity building of this force to take on terrorism and inter-provincial crime. Some of the elite force/Quick Reaction Squads need to be seconded to the FIA, since they will primarily be utilized in Counter-terrorism and violent cases that should come under the purview of such an FIA.
Beyond that there is a need to stop 'negotiating' with the Madrassa's and set up a deadline for compliance and regulation of all Madaris with government set minimum guidelines. These madaris have possibly millions of people studying in them, and the government cannot afford to ignore and not regulate institutions that potentially impact such a large number of Pakistanis.
But improving law enforcement and domestic intelligence is the key here, and that is not going to happen so long as the politicians at both the Federal and provincial level control the institutions that would most effectively combat terrorists, extremists and their sympathizers and supporters (some very powerful), and refuse to make them autonomous lest their own crimes are found out.
Of course, a comprehensive policy needs to be established but this chaos, utter chaos where a number of groups, some very organized, most having a very flexible structure and some offshoots with some even autonomous groups operating as terror outfits in the country has never been seen anywhere in the world.
No other country faced a challenge so severe where there were so many different offshoots targeting the state and people.
Secondly, even though we like to say that the nation has a definitive stance against terror and people are resolute against it, it goes without saying that there's an utter lack of rational opinion amongst the people as to what is the right way to handle this. Case in point being the drone attacks. The US and other independent organizations/think tanks seem to say that they have a very high success rate, the right wing media has generated so much negativity on this (not out rightly unnecessary though) that people somehow believe that stopping drone attacks will stop the waves of suicide bombings. IK, a whole sidelined political lot and many a people hold this view. In actuality even if this works, this would mean that the targets were in reality militant groups with radical ideas and beliefs who we'll be tolerating.
Thirdly, an utter lack of organizational presence in the regions where the whole mess has emanated from, both historically and present as well. The regions have remained lawless, there is still significant presence of these "elements", otherwise we wouldn't have been seeing this and however we want to portray the locals as patriotic Pakistanis, it seems that there's a huge mix of nationalities in the militants out there. Intelligence and law enforcement presence has been weak at best throughout history and non-existent in most ways.
Fourthly, a political upheaval or instability stems chaos in other areas including economic instability and will never have a positive outlook on the militant scenario. At least we're seeing a consensus and resolution amongst the higher echelons of power although it would have been and should be much more befitting if they provided inputs to the policy rather than leaving much of it to the military, which you might not want to accept it, has hardly ever been successful in handling these areas. You might like to consider that the Soviet War was handled successfully but as we're seeing the fallout was never calculated and we got involved too deeply. Then we got in with the Taliban government and that didn't work out well either. Then we went in to fight in 2003 under pressure, didn't really fight much and signed peace treaties which did not work out as well. Comprehensively, the military has never been successful in the region. Short run success that results in a long term chaotic failure is no success. The higher echelons of power have owned the war and not run it, this has been a serious policy failure but this has been the outfall of our traditional political equation.
Fifthly, the point about PML-N and the whole SSP/LeT links, even I feel has been grossly exaggerated. They've relied on them for political support and will never tolerate an armed operation against them, but this somehow does not mean that the militant ideology has found sympathies beyond what we see in ordinarily religious Pakistanis as well. They should have and now must disown it, disconnect themselves and clean up this whole mess once and for all.
Sixthly, the FIA plays absolutely a very small role in all this. It has not been it's role and it is not supposed to play a CT role either. The institutional rivalries between the IB and ISI are to blame much for the lack of a coherent policy and ineffective investigations and lack of coordination with law enforcement. People in the IB, the higher ones who come through its hiring, still have bad blood between them and ISI since Musharraf Sb's picks for DG IB, Talat Munir and Bashir Wali inducted hundreds, if not dozens of retired ISI officials and the number of military guys on secondment sky rocketed as well. The two organizations have hardly ever been super-cooperative with each other, but the early part of the last decade sure messed up things a lot. Moreover, military apologists here always try to portray facts using the self-righteous and all-competitive image of the military rather than laying out the real facts. It is clear that the ISI has been more or less played not a very successful role (leaving aside the fact that the IB should be playing the domestic role). The lack of IB's presence in FATA (utterly no presence whatsoever) has been acknowledged by many as a problem but their domestic network is pretty strong and tight. The lack of information sharing about tip-offs and investigations plays into the hands of the militants. Suppose the IB got tipped off about a possible militant named Ahmad and ISI later gets tipped off about him but the surname Zubair. A better inter-agency coordination would yield results but the ground reality is that there's little or no cooperation other than the JIT's that are formed to investigate events. And even then we come to know that ISI had their own investigation, MI had their own, Punjab CID had their own and what not. Utter lack of cooperation also results from our societal factors of never trusting anybody and the whole selfishness amongst the men in power. Keep in mind also that although NACTA was formulated, the DG selected to be a very competent man (Tariq Pevez), but it is yet to become functional and nobody makes a secret out of the fact that the problem is that both and ISI and IB are unwilling to yield any practical power to it. Yes, a new organization would be weak but a joint collaboration can soon create (and would have created by now had they been sensible since the start) an effective functional joint counter-terrorism body. Also, the ISI is unwilling in any case to let go of it's position as the top most body in this hierarchy that has nothing but no established grounds rather the result of our decades of political manipulations. I happen to have a friend in NACTA, and frankly he's been dismayed with the progress and the reasons are clear.