The publicly released version of the National Intelligence Estimate that Laura mentions below is only a page and a half, so it should come as no surprise that there is nothing terribly insightful in it. ("Breaking news! Al Qaeda is dangerous!") But let's take a look, shall we?
Al-Qa'ida is and will remain the most serious terrorist threat to the Homeland... We assess the group has protected or regenerated key elements of its Homeland attack capability, including: a safehaven in the Pakistan Federally Administered Tribal Areas (FATA), operational lieutenants, and its top leadership.
The FATA referenced here include places like Waziristan, which Mother Jones profiled in an essay and stunning photo shoot in 2004, where the Pakistan government (usually) respects local tribes' claims to sovereignty and keeps only a loose leash on things. Because of the lack of control, the areas are often perfect for terrorist hideouts, a fact the U.S. has known for years — in fact, the emphasis on the FATA in this NIE matches policies from the beginning of the war on terror. Back then, we paid locals for turning in alleged al Qaeda operatives, which merely gave the locals a more powerful weapon in tribal conflicts and filled places like Gitmo with harmless and bewildered individuals who happened to have a well-connected enemy.
Other thoughts from the NIE (which is available here):