The would-be terrorists made mistakes: the quantities they sought were so enormous - and the reasons they gave for buying them so unbelievable - that suspicions were immediately aroused. In addition some experts doubt that their plot could have worked.
Prior to 9/11 al Qaeda seems to have had some very bright and evil people. Some died in that attack, others died in Afghanistan or by assassination or have been captured. Zawahiri may be the smartest of the group left at large, but he seems to spend most of his energy hiding.
This story suggests that the bench may be thin, something I've wondered ever since the spectacularly incompetent "shoe bomber" effort. Al Qaeda has no problem attracting canon fodder, but it may be failing to recruit and retrain the most dangerous operatives: educated, intelligent, creative, cruel and viscious fundamentalists. One in a thousand adults may combine creativity and intelligence, but these may be inversely correlated with fundamentalism and cruelty. A relatively small talent pool limits Al Qaeda's capabilities.
This also suggests a reasonable strategy. The US employed Russian physicists after the collapse of the USSR, in part to keep them out of dangerous pursuits. Interventions which divert talented individuals from al Qaeda towards more wholesome pursuits will not make al Qaeda and its children vanish, but it will make them far less dangerous.