Though all this is history now, with more than 10 years having passed by, some crucial questions remain unresolved. In the recent study "Anomalies of the air defense on 9/11", published in October 2012 in the "Journal of 9/11 Studies", some of these questions are covered in great detail. You can read it here:

http://www.journalof911studies.com/resources/Schreyer-Vol-33-Oct2012.pdf

Now a video has been released, explaining these findings:

http://www.youtube.com/watch?v=vNM3GQWx83Q

Core of the argument: The flight routes of the fighter jets scrambled on 9/11 show a pattern of deliberate diversion.