Great post Aero (as always)
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The thesis brings up the most important question per the page 15 recommended Net Centric Combat Management process. That is, you have the synergy from the Join Tactical Command down to the level of assets within different services. For the US Military, the net centric operations work fine down to each soldier or each asset. How would this work for the Pakistan Military and what are the big gaps?
In my opinion, the gaps come in at the asset level. Whether its the Navy or the Army, what you really need is a much larger air-arm so that Army and the Navy can carry out their operations successfully. This is where I've been saying that Pakistan needs more jets.
Whether they chose to continue on with ONLY JFT block II till they find suitable 5th gen platform or want to induct MLU'd F-16's in large numbers. The numbers have got to increase. The net centric architecture would work much better if the air-arm had the ability to dedicate a small force (still in decent size like 3-4 squadrons) to support Naval operations and then to support the Army (again dedicated but yet multi-role 3-4 squadrons), the remainder numbers will ensure air-defense and strike related capability. So a force of about 600 BVR and Standoff capable platforms in Pakistan's case to ensure proper allocation of units. This is in addition to the need for a heli fleet for quick air drops, ground support / troop pickup and ground assault.