Then there's the whole issue of the AQ name getting used by groups that don't have very strong ties to AQ proper.
It's kind of faddish for groups that never had anyone trained in Pakistan/Afghanistan to take the AQ name, because it's got built in notoriety. AQ likes it because they get to take credit for more stuff, and the US government likes it because it makes it easier to sell all these groups as part of The Enemy.
The NY Times ombudsman had a piece on the paper's (and the administration's) focus on AQ, to the exclusion of other militant groups. Worth a read.
Honestly, though? Even if there's a rebuilt training base in the tribal regions, the odds are waaaay against a terrorist attack with nearly as many civilian casualties as 9/11. Since that happened, they're just not going to be able to hijack a jet and run it into a building.
They got one over on us, but it's the sort of trick you can only do once.