The disastrous and failed military operations of the Pakistan Army in FATA during Musharaf years are a testament to the loss of fighting ability.
Firstly, let me point out that both the WWII-era Soviet Military and the Wehrmacht were heavily represented in the political spheres, in fact their presence in social life was to the point of being pervasive.
That being said, let me move to the actual point I want to address. The marginal success of military Ops during Musharraf's era were not due to the fact that Musharraf was the president and removing him magically made them fight better. There were a number of reasons, some of which I shall note briefly.
1. The operations were limited in their objectives. The PA was not looking to establish complete control, they were looking to expunge foreign fighters. The TTP had not yet been formed and so local fighters were seen as misled tribal youth that would just go back to normal life if the foreign influence was removed.
2. The PA was still very much a conventional force then, they tried to fight a low intensity conflict utilizing the techniques that were developed to be utilized against a professional military. Classic mistake that all militaries new to LIC make, the Russians in Afghanistan and Chechnya, the Americans in Vietnam and Afghanistan, the French in Vietnam and Algeria, the Italians in Libya.
3. The operations did not enjoy public or administrative support. The MMA Govt in KPK was very openly hostile to the PA and facilitated the extrication of fighters from SWA. The public also condemned it as a military campaign against "our muslim brothers". Resultantly, the operations were wound up as quickly as possible as soon as some basic objectives were met, there was no greater plan to consolidate gains.