There's actually an interesting exercise in logic available here.
The easy step you took is the obvious one: The 911 attack was well conceived and boldly executed. Therefore we can't write off Al Qaeda as a bunch of doofuses.
But what if overwhelming evidence leads us to believe that Al Qaeda ARE a bunch of doofuses?
Then we may be logically be led to the much more interesting and troubling conclusion that either Al Qaeda didn't do the 911 attacks, or they did the 911 attacks with a lot of special help.
Mark W.
Or, as Occams Razor would insist, they simply were crafty without being necessarily technically brilliant.