A. Michael Moore is a fat idiot. No argument there.
B. I've answered your "What should Bush have done?" question in several posts in this thread. If I was Bush that day, my first order, given the knowledge that now 2 passenger jets had been used to bomb the WTC, would have been to scramble jets to protect the nation's capital's airspace from further attack. Based on the well-known timeline found at thousands of websites (do a Google on 9-11 + Timeline), it's apparent that Bush had over 30 minutes to make this decision that might've saved the Pentagon. He did not do this.
I don't blame Bush for the attacks themselves nor think he could've prevented them from occurring based on what we know. I don't blame him for the Pentagon, since there's no guarantee that anything he did could've stopped that either. However, by doing nothing, he insured the Pentagon attack's success.
Okay, you were the President knowing only two planes had been crashed into the WTC, and you scrambled jets to protect the capital. How many jets did you scramble? Who controlled the airspace, the FAA or the Air Force? From your certainty despite the lack of information, I guess the Air Force would have been ordered to shoot down every aircraft that was not diverted from the D.C. airspace. How many airplanes would have to have been shot down to ensure you got the one highjacked and headed for the Pentagon? Or are you suggesting that your military would have had perfect coordination and communication with the FAA at the area airports and all of the airplanes in the area so that you could discretely identify the one threatening aircraft?
Would you also have scrambled fighters to defend all nuclear power plants, chemical production plants and other potential targets for terrorists? Why didn't you put the military on world-wide alert since you couldn't be certain the attacks were limited to U.S. targets? With 20/20 hindsight of course you wouldn't because you know that only the capital and New York were targeted. But why would you implement plans to defend only the capital and not the rest of your nation? How would that have playied in Peoria and in the media? If you had scrambled fighters to protect everywhere, and an innocent aircraft was shot down, how do you think the public would have reacted and the mainstream media would have reported it?
When would you have had discussions with your military commanders to get their assessments of the situation? What if they had told you your desired reaction would be ineffective? The bottom line is that the President did not have sufficient information to implement any actions that could have prevented the 9/11 tragedies. The attack on America came from a direction in which we were unprepared. Despite your heroic expectations, our military is not in constant standby mode where they can prevent attacks on a moment's notice.