Pakistan has to decentralize security - which means we have to focus on capacity building of local law enforcement, provincial/civilian intelligence and making civilian security forces politically independent, better trained and much better paid.
In a country of 180 million, with poor controls over material that can be potentially used for explosives, and poor control over porous borders with Afghanistan and Iran, it will be almost impossible to tackle terrorism and extremism (small local cells especially) with a centralized military and para-military force.
It is certainly not the ISI or PA that has a 'thana' in every city, town or neighborhood - it is the local cops, and they have to be focus of reform to become Pakistan's first line of defense against terrorism and extremism.
It is the local cops who have the best feel for their neighborhoods and residents, and the best ability to observe and respond to 'suspicious activity'.
The reforms and ideas behind the successful Motorway Police would be good model to follow.
I would also argue that the FIA and IB need to be merged with their provincial equivalents, with provincial HQ's, to minimize red tape and better share data and information. The two organizations need to be taken away from the Interior Ministry and put under the control of a bi-partisan parliamentary commission, perhaps similar to the judicial commission.