Unfortunately, the real truth lies somewhere in the middle. Much of the referred article is obviously written by people with a poor fund of facts and just a bit too eager to assign conspiracy as the cause, while OTOH, Bodecea is a bit too eager to utterly dismiss the few glaring incongruities that do not make sense in the 911 saga. Let's take a look at them:
1). The story that the military was conducting rampant anti-terror training that day is something rather irrelevant whether it is true or false. In the official story, military jets in the area were misdirected over the mass confusion as no one had really dealt with this situation before and many mistakes were made. In either case their training or not has not and is not necessary to explain the success of the missions.
2). The airline pilots were obviously not in on their own deaths and at that time, not knowing the fatal intentions of the hijackers, there is nothing strange that they were able to seize control of the planes using fear, confusion, lies and murder. That would not be possible now.
3). That the terrorists were only trained to fly small private planes is a new story to me and conflicts with the official report, however, that said, the basic operation of jumbo jets are the same. Indeed, with the power controls, the jumbo jet is EASIER to steer and fly, and that is all the terrorists needed to know, the basic steering of the jet, the throttle, and landmarks to guide their way. No understanding of the complex instrumentation or avionics was necessary. But I think it is pretty certain that a few of the terrorists had a passing understanding of basic jumbo jet operation, enough to take it out of auto pilot and steer them into the buildings. You only needed ONE person per plane to know these things and Mohammad Atta was one smart cookie.
4). The actual construction of the Twin Towers is not as described: The main support for the buildings was the central column, which both jets missed or avoided. The outside skin of the buildings you saw was a thin skin of structural steel and windows with little strength of its own. It was primarily held up in place by being tied to the central column through the spans which held the floors. In-between, the floors were essentially "hung" between the two as platforms. The interior steel structure was protected with a spray insulation since then proven ineffective in this case and would have been blown off; it was only designed for natural occurring fires.
5). The lack of better video at the Pentagon is disappointing and a survey of the actual camera angles would shed better light, but for national security reasons, we will have to accept this as the best video they got. But if this was a frame, why release any video at all?
6). The disappearance of the two jets into the Towers does NOT conflict with the known construction of either the buildings or the jets. The structural concrete was at the CENTER of the buildings and within the floors and would have only sliced the jets up into sections, which would not have changed anything seen from outside. The jets are built of 6061-T6 aluminum alloy which is a composite of many metals including titanium, magnesium and iron, with a tensile strength of over 40,000 pounds per square inch. That multiplied by the high inertia of the jets at full throttle multiplied by the small cross-sectional area of the nose and wing leading edges would have further magnified the force into one capable of cutting through the outer skin of the buildings consistent with observations. Obviously it happened, we see it, and no "special plane" could have been build, loaded with passengers and flown into the air. Anything significantly stronger would be too heavy to be airborne. And the outlines of the jets puncturing the outside of the buildings of the videos is consistent with all of this, no Willie Coyote needed. Without the support of the central column, the outside of the building was as flimsy as a deck of cards and had little strength on its own. The buildings were designed to be strong with everything interconnected together and to absorb and deal with normal, smaller, accidental plane collisions and fires, magnitudes less than what actually happened. No one ever expected a large-scale commercial jet flown by a top pilot could ever accidentally fly into one of these buildings.
7). The impact at the Pentagon might have been possible to avoid ground effects if the jet were angled downward getting close to the ground only in the last few hundred feet and indeed, this seems consistent with eyewitness observations and that some ground effect might have actually pulled it as low as it actually hit the building. Very very low.
8). That there was no evidence of wings hitting the sides of the building or any residue of the plane or passengers is harder to explain but not impossible. Since the Pentagon WAS a heavily reinforced THICK concrete and steel building of the highest order, what SHOULD have happened is that the wings would have been utterly shattered on impact, rebounded and folded back along the fuselage while the entire plane literally crumpled and exploded in total focused annihilation. The jet would not have penetrated the building and just as seen in the one video, the jet would have imparted the ENERGY of the total impact and explosion against the outer wall with the wall pushing back. If the energy of the plane impact and explosion was even slightly greater than what the wall could repel AS A SECTION, that section of the wall would have been knocked inward according to Newton's simple Third Law of Motion, and that seems to be exactly what happened in the pictures. There literally would be nothing left of the plane but tiny pieces and dust. No bodies would have survived.
9). Obviously one of the missing jets WAS accounted for and was taken down into the ground at Shanksville. This was corroborated by last minute calls made by passengers. That there is no evidence other than a hole in the ground is confusing, but again, the earth would not have given much way and the jet would have explored to smithereens in the violent compression/explosion. If anyone doubts this, all they need to do is arrange to have a similar jumbo jet flown robotically straight into the ground at top speed THREE times. If ALL of them fail to end up similar to Shanksville then now you have a question.
10). It takes no violation of physics to explain the melting of steel; the jet fuel combined with materials present inside the buildings would produce an intense fire with sufficient heat that after the explosion of the impact blew off the fire protectant foam, the heat from the sustained fire would have over a period of 20 minutes or so would have been enough to SOFTEN the long spans of steel holding each floor up to the point that the floors would have sagged under their weight, pulled loose of the hangers at each end and started to fall. First one dropped onto another, now the two or three would have easily overcome the strength of the floors below it not just from the multiplied weight, but from the energy of absorbing the impact of the floors above dropping on them which for a moment would be ten times their weight, and very quickly, the process would have been self-sustaining and impossible to stop, and this pancaking effect has been corroborated by witnesses there at the time who both saw and heard it. The central tower would have been damaged and fractured, collapsing, and the outer skin buckled by the lack of stabilization and support, and the buildings would have fallen just as it was seen.
11). The other third building 7, that it later fell is not too hard to understand considering the close proximity, possible damage from the other building's impacts and collapse that the damage, if not the subsonic shocks of the Towers falling, was enough to bring this building down. Remember that ALL THREE were tied together by a common substructure below ground. The little puffs of smoke seen in the one video were probably nothing more than the internal collapse taking place inside at or below grade blowing smoke forced up through one of the stair towers and out of the building.
12). The assertion that the airline was somehow "in on it" by letting all of the hijackers on without any manifest is absurd--- --- especially because doing so would have only ADDED to the suspicion and difficulty in explaining, THE ONE THING any conspiring body would have SOUGHT TO AVOID.
In conclusion, as a person with aviation and avionics experience and knowledge, a background in physics and having studied the 911 report in detail, there are no laws of physics being violated here nor needing violated, few loose ends and no conspiracy needed, and no one, Bush or otherwise, needed to go to these lengths of destroying the Twin Towers and damaging the Pentagon and the loss of all those lives to have effected a sufficient reason to justify the attacks against Iraq and Afghanistan, ESPECIALLY considering that we got nothing out of it! Had we seized their total assets of oil and money, you might make me believe it a bit more.
The one thing most difficult to explain not even mentioned in your article was the videos showing what appeared to be an additional fuselage or long appendage body attached to the underside of one or both jets which should not have been there. It is somewhat consistent with some military applications, but then, these would have been glaringly obvious to all at the airport, no "switching of planes" in the air was possible unless the entire airline industry was in on it, and the appearances of these added bodies may just have been video artifacts.
IN CONCLUSION: the original story of the attacks stand as accurate, the article above is specious in its assertions and inconsistencies trying to make a case without real facts to support it, and while not everything adds up perfectly, no grand conspiracy is needed at all to explain and accept it. But it never hurts to keep an eye on big brother.