First and foremost is why didn't Andrews AFB fighter jets (10 minutes from DC) ever leave the ground?
How could the second WTC tower hit be the first to collapse, especially when its massive fireball meant that a large amount of that plane's fuel burned outside the building?
How could Bush say that he saw the first plane hit the WTC on TV, when no such footage existed at the time?
How could all flight recorders remain unfound, yet Mohammed Atta's paper passport was so easily recovered?
There are also dozens of issues that I must categorize as rumor level, because I've not been able to verify them well enough, like the names of hijackers belonging to people who are still alive, or the lack of evidence of plane wreckage at the Pentagon, or the wreckage of Flight 93 being scattered for 3 miles implying that it was shot down, or passenger lists not listing the hijackers, etc.
Similar credibility stretching occurred with the OKC bombing since it is clear that no single truck loaded with ammonium nitrate could have caused damage of that magnitude or of that effect to the Murrah Building.
Too much precedent of lies used to start or escalate wars exists, including the Northwoods document <http://www.gwu.edu/~nsarchiv/news/20010430/> that detailed how the Joint Chiefs of Staff described ways to make it look like Castro had attacked our planes or ships, when it was to be our own military that would fake the attacks. Or the Gulf of Tonkin incident which launched the Vietnam war with lies that the North Vietnamese had attacked our ship in international waters, when the truth was that our ship was in North Vietnam's territorial waters shooting at their shore bases.
Even Pearl Harbor is now suspect as to what FDR knew, with Robert Stinnet's "Day of Deceit" saying that not only did FDR know what would happen that morning, but he intentionally did not report what he knew to the base, so that he'd have the event he knew would change the anti-war sentiment of the populace.
While I'm not ready to conclude that the USG intentionally let the events of 911 happen or were complicit, (mainly because I can't bear to face it), I surely can't be blind enough to consider it outside the realm of possibility either. There are too many questions and too much precedent. Besides, it seems all too clear that the USG had an agenda laid out well before 911 that was well served by the events of that day.
--tully