I think they had their eyes on Iraq and Afghanistan because of previous US involvement in those places that didn't result in total subjugation. They would have preferred Iran, but Iran would have been too difficult to invade or get the justification for to build the Coalition that helped invade both Afghanistan and Iraq.

The US had been fucking around in both countries prior to 9/11 about a decade before and never saw return on their investments. Plus, by choosing those as targets, they could go off existing intelligence and experience from previous adventurism.