AQ's key leadership could hide there when needed and weapons were freighted through also.
Iran, however was deeply concerned that the Kurd-AQ Ansar al Islam would cause rebellion in the Kurdish areas of Iran. There are more Kurds in Iran than Iraq. So, to make sure AQ (and Zarqawi) behaved, two AQ leaders became guest hostages in Iran: Saif al Adel and Saad bin Laden. Now that AQ has shut down its Iraq operations Saad bin Laden is needed more in the Af-Pak theater. Saif continues to coordinate logistics and money laundering.
Yes, Pakistan (and the Afghan/Pakistan border area) does seem to be the hot spot.