This article hits it on the head.
Who's really locked up in Guantanamo? - Los Angeles Times: "What the administration doesn't want to face is that, as the small fish were taken to Cuba, Pakistan arranged escape routes from Afghanistan for more dangerous jihadists � presumably those with cash or connections to Pakistani intelligence services � including several hundred flown out of the city of Kunduz before it fell to U.S. forces. The Pakistani military maintains close links with Al Qaeda-linked militant groups created to wage war in Kashmir and Afghanistan, and the Taliban continues to hold sway over Pakistan's tribal areas on the Afghan border. Bush should devote the resources needed to stabilize Afghanistan and tell Pakistani President Pervez Musharraf to end, finally, the military-Islamist alliance that has made his country the new home base for Al Qaeda and the Taliban"