Right... some men equipped with boxcutters managed to bypass the most heavily militarised country in the world and then as luck would have it their passports were able to be retrieved perfectly intact from the debris a week later. 
Wrong, some men equipped with boxcutters managed to bypass $10 an hour American Airlines and United employees just starting their morning shift on a lazy weekday afternoon.
You know, there aren't U.S. Army/FBI agents with machine guns and grenade launchers INSIDE passenger airplanes, right? That whole depressurization, shooting civilians, and cost thing sort of makes it not really practicable. But go ahead and keep thinking that 3 guys working together with boxcutters, taking over a plane in the year 2001 was some sort of crazy impossible feat.
Remember, at the time, people were trained not to resist with hijackers, because most hijakings up to that point involved the person asking for money or making incoherent political demands and demanding the plane be flown to wherever. There's a reason the first reaction of most people, whether they be FAA or military was along the lines of "What? A hijack? We haven't had one in ages" or "Who is it? D.B. Cooper?" or "Oh wow that's cool" (that last is actually a legit recorded reaction of one U.S. soldier during the initial stages).
You make it seem like the entire U.S. was on full alert and some guys with box cutters managed to storm their way on the plane, slashing through the Delta Force or some crap. It's called "social engineering". They used social engineering to take advantages of lapses in security, the way most social engineers do.
as luck would have it their passports were able to be retrieved perfectly intact from the debris a week later
By your "logic" people surviving building collapses should be impossible too.
Do you have any statistics on what % of passports survive a plane crash or what % of documents survive a building fire and collapse? Because unless you have those, your statement is meaningless. There 18 hijackers. 4 passports out of 18 survived. One of those passports was because it wasn't on any of the flights due to a botched luggage transfer (and if you think airlines botching luggage is some wild improbability, you need to get a clue).
Of the remaining 3, two were on United 93, which just had the crash and no accompanying building fire and collapse. Only one was form the NYC/DC incidents.
Before you punch holes in other theories, try punching holes into ones you believe. It will make you smarter and less susceptible to stupid conspiracy theories.
