and the PA wreckage indicates the plane was shot down (how else would there be no real crash site and debris scattered for miles?).
Okay, I can't explain everything (at least not at this moment,) but I can easily describe this:
There
were terrorists who had control of the aircraft, and so it
was shot down to prevent it from being used for any more aircraft attacks. But really, think about it. If the government can get away with saying that it wasn't shot down and that the people on board bravely resisted the terrorists, but unfortunately getting to the controls just seconds too late, instead of "as a calculated decision, we murdered 160 Americans," I wonder which one they'll go with. It's low, it's filthy, and they should probably be tried in court, but they didn't make it up entirely, or at least like the conspiracy suggests.
Also, as Keithz says, I imagine that an airplane running 500 km/h into a reinforced concrete wall designed to be missile-resistant wouldn't stand much of a chance. Perhaps they didn't find your typical crashed airplane body crumpled into there, but it probably was there. Either a couple kilometers away, or as a very, very fine powder.