I think the US (along with other members of the free world) probably did have an agenda and contingency plans regarding Saddam Hussein before 9/11. But I believe this developed long before GWB was elected to the presidency. And who knows what would've happened had not OBL carried out his plans first. I doubt the world would've sat still for Saddam to develop nuclear weapons. Just as I do not believe the free world will sit still for Iran to develop their nuclear weapons.
No doubt, any good command will always have contingency plans dealing with any nation in its area of responsability. However, I still say that after Afghanistan, Saudi Arabia should have been the target. It did attack America and still does, daily. Furthermore, the Saudies have WMD, missiles to deliver them (at least to Israel and maybe Cairo) and told the UN nuclear inspectors to shove it when they wanted info on their nuclear weapons programs.
Simply put, we could not leave an Unconfined Saddam on our flank. Containment of Iraq was breaking down as the Oil for Food Scandal shows. We needed a Terrorist Kill Zone, Iraq provided it. We had the political and legal justifications to take out Saddam. He was in violation of the 1991 Cease Fire. For the US in 2002, the strategic logic of Iraq is inescapable. We could NOT tie up major military forces else where in the world and leave Saddam unfought on our flank. Saddam's Iraq was a lingering, festering boil on the world's body. One way or another it had to be lanced.