I think we actually did **** up the top-tier command chain in al Qaeda pretty bad. But then, that's almost certainly not worth much, 'cos the lower tiers would actually be the functional leaders, orchestrating everything but the really huge things. I mean, it's really unlikely bin Laden personally masterminds every bomb that gets placed, or even necessarily knows anything specific about a given local division at all. Guerilla organizations don't work that way, it'd defeat the whole purpose of the cell system. He's a figurehead and a financier, basically, and most of the guys we caught were technicians and the like. The beauty of a system like al Qaeda is that every part is inherently replaceable, and that you could destroy 90% of the system without crippling the last 10% substantially, rendering the organization functionally immortal unto the point when it serves no more purpose (the cause is either finally won or finally lost), and probably a little while after that. At this point, the US has probably eliminated more around 5%- at best- and they've probably replaced what was lost by now and then some.
The downside of this, of course, is that organization is crap. I mean, if you look at it, the 9/11 guys pretty obviously went in with no planning and no caution whatsoever, and the whole thing could have been drawn up in about fifteen minutes by somebody who didn't even particularly know what they were doing. Anything that involves more than a couple of cells working in close coordination is simply out of the question. For this reason, really advanced attacks and nukings and all that stuff... just aren't gonna happen. For an organization that's based mostly on survival and sniping occasionally when it can get the chance, that's an acceptable payoff. But it means that really massive terror attacks are going to be a rarity, and they're certainly not going to be part of any greater plan.