The problem with that website is that it takes the slightest hint of circumstantial information or conjecture and twists in into definitive proof. For example, the fact that a flight attendant only saw 4 hijackers instead of 5 can easily be explained by pointing out that maybe she just didn't see one of them.
The author of the website also cleverly mixes in a real news report that says nothing to support his conclusion with a link to a website (http://www.americanfreepress.net/051302/FBI_Admits__No_Evidence_/fbi_admits__no_evidence_.html) that makes a claim of events using poorly worded statements of conjecture, rather than actual quotes from the FBI that say what he's saying the FBI said.
From example:
Conjecture does not equal fact. Saying its "in doubt is whether those 19 men were actually plotting anything" is not the same as saying "those 19 men were not actually plotting anything".
Another link (http://www.newyorker.com/fact/content/?011008fa_FACT) cited as a source critical of the 9/11 investigation uses conjecture by unnamed sources as evidence and was published barely 3 weeks after the attacks, before the investigation was even close to being complete.
So, upon carefully reviewing the evidence, I can only conclude that the entire article (http://www.whatreallyhappened.com/hijackers.html) is nothing but fabricated stupidity.