Many of the federal representatives who rule over NA are from NWFP and that creates some resentment. And there are some issues over resources but I don't know enough details about this aspect.
I don't think that the administration of NA is done by any credible politicians, it's just bureaucrats, with little interest in the area. Which is why its important to devolve power to the local levels and away from Isb.
I'm not aware of any known resource issues despite living there for 3 months. Unless you could some random person having a problem with 1 person from Pakhtunkhwa, and its getting some type of coverage. Also, lets not forget the incredible diversity in the NA where there are competing local interests as well.
When all is said and done, folks from Islamabad do not have the expertise/understanding to effective administer NA.