I think that you highlighted the very issue that /u/Velvet_Llama was alluding to: the odd observations are just that. They don't string together in any cogent narrative in the same way the official story does.

Okay, there was training operations that day.... What does that mean? The government perpetrated the attack and also planned for an operation to stop their own operation and did so on the very day of the attack to cast suspicion on themselves?

Okay, the collapse of WTC7 is a bit unique... what does that mean? Did the planners of this operation think that taking down four planes, two towers, and partially destroying the Pentagon wasn't enough to justify a war so they felt they needed to take down a building, not bother to hit it with another plane, kill exactly zero people doing so, and then make such a small deal of its destruction that most New Yorkers don't even know that it was part of the attack?

Your point about invading the wrong country also doesn't quite make sense. Okay, we invaded two countries from which none of the attackers originated... how does this fit with your narrative? If it was an attack planned and perpetrated by our government why wouldn't they just draw up a list of Iraqis and Afghanis instead of hoping that they could later make a tenuous case they these countries were somehow involved?

Tell me narrative that makes more sense than this: A group of fanatical Saudis highjacked a group of planes and crashed them into buildings, causing massive destruction of them. Some of the occurrences of that day were unique in history (like buildings collapsing due to fire) but it was a day full of unique occurrences (fully loaded passenger jets crashing into sky scrapers). Retrospective models have accounted for most if not all of these strange occurrences. The immediate response was to invade an easy target country as a near gut reaction to being attacked (the perpetrators were Saudi but we couldn't attack them because they are our ally so we instead attacked Afghanistan because the mastermind behind the attacks was purported to live there). During the year or two following the attack politicians who long wanted to invade Iraq for its oil wealth were able to take advantage of American anger and drum a case for war with Iraq. I would also like to add that I believe there were some major intelligence failures that could largely explain odd behavior both before (such as hints that government might have known something was in the works but failed to take it serious enough to act on) and after the attack (lack of transparency in the investigations of the attack).

Tell me a story that makes as much sense as that and explains as many of the observations and you may very well convince me. Also tell me which observations don't fit with my version of the events.