Walking It Backwards
Experienced golfers know that one way to learn about a new golf course is to walk it backwards, because a lot of times that will make it obvious why the designer put sandtraps, ponds or trees in particular spots.
So it works with conspiracy theories as well. Let's grant the producers of Loose Change their notion that the government came up with a "false flag" operation in order to get the transformation of the military that the PNAC desired.
Why four planes? Why hit both World Trade Center buildings? The 1993 bombing targeted just one tower, although the terrorists hoped that it would topple into the other. Why hit the Pentagon?
More than that, why, if you were going to hit all three of those targets, why would you hesitate to use the actual flights? Obviously you aren't trying to spare lives at this point. Maybe the problem is that even the 9/11 conspiracy buffs can't come up with a logical reason why anybody other than a Muslim fanatic would deliberately steer a plane into a building knowing he would die in the process?
So walking it backwards, we see why the WTC planes had to be phony drones (and a cruise missile/helicopter/A3 Skyhawk--correction, Skywarrior/who knows what at the Pentagon). And if the planes were phony drones, then it's important to destroy the two World Trade Center towers, so that nobody ever gets too close a look at the planes.
See how the movie is starting to make more sense when you start with the conclusion and work backwards to what "had" to have happened? Now we can see why a jet "couldn't" have hit the Pentagon as well--because unlike the WTC planes, it wouldn't be destroyed by the collapse of a 110-story office building.
Now we can see as well, why the "cellphone" calls "had to be" fake. Obviously if Betty Ong's phone call was for real, that's pretty strong evidence that she was on one of the planes that hit the World Trade Center.
But if the three planes that actually reached their targets were drones, what does that mean for Flight 93? Having it deplane in Cleveland some 200 passengers dovetails (or rather, they pretend it dovetails) with the number of passengers missing on the other flights.