I've always been bothered when people try to argue missiles as the sole cause for trade center towers one and two, but I've never been quite sure why until today. I don't believe the planes to be the sole cause either, but that's a different post for a different day. Here's my theory:

What better way to execute a massive false flag than by hiding it behind a simultaneous genuine terrorist attack? There's been plenty of reasonable arguments for isreali/saudi/CIA funding of the hijackers, and I tend to put my money on "false-flag by proxy" ideas when it comes to buildings 1 and 2.

The twin tower events had the greatest shock value and largest loss of life, virtually guaranteeing that coverage would focus almost exclusively on them. This would keep analysis of building 7 to a minimum.

The wtc7 and pentagon events made a good deal of people very happy. Here are a few of the parties that stood to benefit from the that event:

-Documents housed in wtc7 might have lead to the successful prosecution of several corporations (including rite-aid and motel 6), but without an open/shut case, the prosecution decided to settle these cases out of court, likely saving these corporations from bankruptcy and criminal proceedings.

-Silverstien is estimated to have collected on ~800 million on wtc7, and (as acting owner of all 7 WTC buildings) is estimated to collect up to ~4.5 billion for buildings 1,2,4 and 5. Its worth noting that nearly 383 million in mortgage bonds where still owed against building 7, making an insurance claim particularly profitable. Furthermore, silverstien showed interest in buying out bond-holders at face value. Thats one hell of a way to get out of a structured payment plan and still turn a profit. All things accounted for, the WTC complex was built between 1975 and 1985, at a cost of ~400 million, which wikipedia estimates at 2.3 billion, accounting for inflation. That is a 2.2 billion profit (averaged across the various lease holders) in 26 years, for a 49% profit margin, and that's not even counting the insurance on buildings 3, 6, and 7; as all 7 were considered damaged beyond repair.

-The WTC as a whole was a money pit. It has been said that the WTC complex cost the NY govt millions in subsidies every year, but I dont have a reliable source for that claim (if anything has a source for this, please link it to me!). With some interventions by rockefeller, the WTC plans were drawn and proposed to (and sequentially approved by) the port authority of new york and new jersey in 1962. The entire project eventually became a financial liability, and would later be re-leased (again) to silverstien in january of 2001, less than a year before the complex was destroyed. The only reason the towers were not demolished long before 9/11, is the presence of asbestos in the construction. NBC (of all groups) reported on this. To give some perspective on the cost of asbestos removal, an example of a building at 55 broadway is often given, with an estimated cost of 70 million. 55 broadway has a floorspace of ~346,000 sf, while the north tower had ~1.9 million sf. One can imagine the sheer cost such a project would imply, definitively putting the entire investment well into the red.

-8.5 trillion in unaccounted DoD/pentagon funds, between 1996-2012. This money is not "missing" in the strictest sense of the word, but it might as well be. The funds were spent by the government, so this is a case of fraudulent accounting, rather than outright theft. This guy does a pretty good job of explaining the situation in a forum post. Donald rumsfeld admitted to 2.3 trillion in unaccounted for pentagon spending literally the day before the WTC event. "Most of those killed in the [pentagon] office, called Resource Services Washington, were civilian accountants, bookkeepers and budget analysts. They were at their desks when American Airlines Flight 77 struck." - South Coast Today/Pittsburgh Post-Gazette (12/20/01)

My conclusions:

All of the above motives point towards a different scenario for the pentagon and wtc7 attacks, when compared to the twin tower attacks. Those pushing claims that the footage of planes hitting the twin towers is faked, are seeming trying to discredit the idea of any missile involvement whatsoever. The nuke theory also seems like purposeful disinfo, as the cancer seen in 9/11 survivors is completely explainable by the levels of asbestos seen in the area after the attacks. Building 7 reportedly (according to an un-cited wiki post) collapsed only 6 seconds after being "struck by heavy debris," meaning no reasonable argument for fire as a cause can be made. At 4:20, the stock market announced that it would remain closed the following day. At 5:20 (when building 7 fell) there were still active fires carrying smoke many miles from the site. This smoke in this picture is heading south, covering a little over 10 miles, beyond which there is only ocean. It would not be hard to use this smoke as visual cover for a missile to cover the 7-10 miles of population between the WTC site, and the open ocean. That would leave only ~500 feet to cover between the smoke of building 1 and the location building 7. My money is on a missile, but I have no proof, only circumstantial evidence, clear motives, and a foolproof method of delivery.

Other sources:

State and City Subsidies Help Spur Construction On World Trade Center Site

Federal Building and Fire Safety Investigation of the World Trade Center Disaster: http://www.nist.gov/el/disasterstudies/wtc/upload/7Bukowski.pdf