In my view, the biggest threat to Pakistan is a surprise missile attack specially a nuclear one. In such a surprise attack, time to respond to the threat is critical. Pakistan needs to think 'Outside the Box' otherwise following others footsteps will get Pakistan no where. So my suggestion only covers this aspect.
1-Satellites, AWACS, ground based radars, slow flying air-ships equipped with long range radars, etc all in a NETCENTRIC system controlling a variety of other systems such as below:
2- 1st line of defence: NNEMP (Non Nuclear Electromagnetic Pulse) weapons in combination with Electromagnetic Forming.
3- 2nd line of defence: NEMP (Nuclear Electromagnetic Pulse) weapons.
4- 3rd line of defence: traditional anti-defence systems.
Everything that flies needs a 'guidance system', and hence the key here is to disable or partially destroy the guidance of the incoming missiles and weapon systems.
An important issue are the Ballistic missiles flying in upper atmosphere would need a large, slow flying, satellite/AWACS Linked aircraft equipped with NEMP and NNEMP weapons. Large Air-Ships flying well inside the territory of Pakistan will do the job. Such Air-ships can launch one or multiple NEMP missiles towards the Ballistic missiles to cover a huge area and literally wipe out dozens of missiles.