Having seen four of the major cities in Pakistan, I think Peshawar is my favorite, both because of the history of the city itself, as well as the attractions around it.
Peshawar has been the cross roads of Asia for all recorded history. Founded 2,000 years ago by the kings of the ancient Gandharan civilization, Peshawar has been visited by Marco Polo, Alexander the Great, Moghul emperors, and Queen Elizabeth. When the Soviets invaded Afghanistan, the mujhadeen gathered and trained in Peshawar on their way to Afghanistan via the Khyber Pass. The money, training, and weapons that the US gave Osama bin Laden to fight the Soviets entered Afghanistan via Peshawar and the Pass.