Pakistan started off with nothing in 1947. Present day India got most of the legacy & development left by the British, while Pakistan got nothing. Considering the fact how America fared in its first 64 years in existence, Pakistan hasn't done too badly.
The people of Gilgit-Baltistan & AJK cannot get Pakistani citizenship, because Kashmir is an unresolved issue with India. Gilgit-Baltistan has been given full internal autonomy though, it just couldn't be given provincial status because of the on-going dispute with India. Btw, my servant in my house in Islamabad is Balti, he left Skardu & got a job in Islamabad, & he has a passport, & is a Pakistani citizen. There are many such examples like that. Similarly, the AJK is technically NOT part of Pakistan, it is like an independent nation, so it can't get Pakistani citizenship. I also do not know which parts of NWFP & Balochistan you're talking about that don't get Pakistani citizenship.
While the author has made some pertinent points in his article, he has basically just shown his frustration more than any real objectivity.