Pakistan intelligence (ISI) was a conduit for the funding of the anti-Soviet forces. General Ahmet of the ISI wired $100,000 to Mohammed Atta shortly before 911, though the Official Investigation said the funding issue wasnt important.
Part of the problem is that there is so much that is unclear about 911.
911 commissioner Lee Hamilton said he felt they where not supported, even hindered by the executive. Getting information was always difficult because they weren’t given the co-operation and support they needed. They where also very restricted by time and money, and they had to fight for what they did get.
There we're also conflicts of interest on the commission. The fact that commission Executive Director Phillip Zelikow was closely tied to the Bush government for example…
"Though he has no vote, (Zelikow) arguably has more sway than any member, including the chairman. Zelikow picks the areas of investigation, the briefing materials, the topics for hearings, the witnesses, and the lines of questioning for witnesses. . . .In effect, he sets the agenda and runs the investigation."
The situation was so bad that Sen. Max Cleland resigned in disgust form the comission because he felt Zelikow was actively covering up for the White House. “It’s a scam, it’s absolutely disgusting” he said in an interview with CNN’s Wolf Blitzer.
The 911 report was effectively restricted to trying to describe the events that unfolded on 911. There was no real investigation of what went wrong in the government or intelligence services
One pretty large controversy last year was the fact that commissioners Hamilton and Keane had strongly criticised the CIA for not giving them taped interrogations of key Al-Quaeda figure Abu Zubaydah.
9/11 Commission Chairmen Believe CIA Impeded Inquiry by Withholding Interrogation Tapes
According to author Gerald Posner, in the interrogation Zubaydah named Prince Ahmed bin Salman bin Abdul Aziz and other important Saudi's as being involved with funding and assisting the Al-Quaeda organisation.
http://www.time.com/time/magazine/article/0,9171,1101030908-480226,00.html
Interestingly, Zubaydah named as his boss the leader of the group of Saudis that where allowed to fly out of America after 911. Here is the declassified FBI report on the flight that names the Prince as the leader of the group on page 11.
http://www.truthout.org/imgs.art_02/saudidocs_2.pdf
Now I guess we will never know what was on the tapes because the CIA for some reason saw fit to destroy them (years after Posner's claim I would add). I find Posner at least somewhat credible because of the fact he had written earlier books to
debunk conspiracy theories around the assassinations of JFK and MLK. So I don’t think it is so easy to dismiss him as a conspiraloon or me for bringing it up.
This brings me back to the 911 Commission. In a recent controversy, Phillip Zelikow specifically asked about Abu Zubaydah, and weather he had referred to ‘Prince Aziz’ during the interrogation. The CIA did not respond!
http://graphics8.nytimes.com/packages/pdf/national/20071222-INTEL-MEMO.pdf
There is also a lot of information about the hijackers’ connections with US military installations, CIA, FBI, Pakistani and Israeli intelligence that has simply been covered up. Page after page of anything remotely interesting in this respect has simply been redacted and withheld, seemingly never to reach the light of day.