Until you can actually show 9/11 was a false flag operation, you can’t get by building a vast plot with vague implications that it was. All the loose ends, things that don’t add up, and odd coincidences don’t get around the basic truth that 9/11 was conceived and conducted as a part of a larger terror campaign by Sunni Islamist fundamentalists against the US. Some of the 9/11 participants were not particularly religious but Islamists often enlist the less devout for terrorist operations. The fact that this brand of fundamentalism was fostered by the CIA to push the Soviets out of Afghanistan is more likely proof of short-sightedness than it is that the CIA staged 9/11.
It is also true that the FBI and other agencies knew significant bits and pieces and their lack of action makes no sense after the fact. Even more damning, there was a PDB in August, 2001 where President Bush was warned Bin Laden wanted to attack the US and use of airliners and possible hijacking were mentioned. Yet the Bush Administration took no action in response.
Much has been covered up. However almost surely most of what was kept hidden was kept hidden because it was profoundly embarrassing to the White House and to parts of the intelligence community. Other details were buried because they would reveal actual national secrets or vulnerabilities. Secrecy itself does not prove that 9/11 was a false flag.
While the invasion of Afghanistan followed directly from 9/11, it took a whole campaign of disinformation about Iraqi WMD and ties to Al Qaeda to build support for the invasion of Iraq. Some of the people involved thought they were framing a guilty regime and appear to have been swept up in their own enthusiasm. They plainly overlooked the truth that had been the predicate of American policy since the Iranian hostage crisis: that a secular Sunni-dominated Iraq is the ultimate counterweight against the Shi’a Iranian theocracy. They also dismissed what Bush I knew in the first Gulf War— that Iraq is a fragile construct which could easily come apart in chaos and civil war if invaded. The supporters of invasion under Bush II appear to have truly thought they would be greeted as liberators. Otherwise they would have occupied Iraq with several hundred thousand more troops as advised by a senior military official in public testimony.
Undoubtedly neo-cons used 9/11 as a pretext to invade Iraq, but that comes nowhere close to showing that 9/11 was a false flag.