Well, since it's in Peshawar, it's kind of different than the other major cities of Pakistan. First and foremost, it's dirtier, but when I visited the campus, I liked it a lot.
The people tend to be really friendly overall, and the college is really nice and well kept from what I could tell outside. They have separate sections for girls/guys, and the campus overall is pretty big, especially compared to Shifa. Personally, I liked the school a lot.
I didn't actually get to see any classes or talk to anyone who currently goes there, but hopefully someone else can help out on this thread.
Khyber rocks. Their hostels are better than any other govt hostel in Punjab. The city is a bit polluted and congested, specially with traffic. Otherwise the campus is great and the reputation and history that comes along with it is also superior to many in the country.
Id say they are equal academically, it only matters if you prefer to be in Punjab or NWFP. They are both in equally hotter weather but both have almost attached hospitals etc. I would take Khyber over Nishtar though as its in a more modern city comparatively.