Don't know if I believe all of what you've presented - in fact, I know I don't, but I do know that:
The first... the very first... radio reports I heard of the events in NYC that day was that a small commuter plane had crashed into the building. I remember that very well.
that,
... the damage at the Pentagon has received almost no media attention. National security reasons, I'm sure.
that,
... there is a huge site in NY, reported on by the national news networks and newsmagazine shows, that holds the wreckage of the planes that crashed there, wreckage the NTS is studying for various reasons. I have not heard any report of a similar site at or near the Pentagon nor seen any plane wreckage there in any of the photos or video taken on 9/11. (Note: If you know of such a site, would you please direct me to it? I'd like to see it.)
that,
... turning off the transponders was pointless if the pilots' only purpose was to hide from the good guys. Aircraft is tracked all the time by conventional radar and so could/were these planes. Most likely, they showed up on several radars in several tracking centers in the eastern U.S. until they... um... disappeared. Therefore, why turn off the transponders -- or bother to report it?
Like I said, I don't believe every single word of this, Nicolas, but I don't believe every single word of the gov'ts official 'spin,' either. I believe the truth lies somewhere in between.