Of course there are masive holes in the official story - fuck's sake, there was a massive NLC strike on US soil while Bush was on watch as President, a breach in US security that really only has a comparison with Pearl Harbour. So yes, I think that there is a cover-up - I think the reason behind it was to protect the asses of the administration because when the attacks happened, they were caught with their pants down, strategically speaking.
As I've repeatedly mentioned, at the time Condi was NSA head, was a Cold Warrior and believed that the biggest long term strategic threat was from Russia; there was an inbuilt bias AGAINST the intel and analysis provided by the outgoing Clinton administration, as well as against the various appointees in the CIA, FBI etc; finally, George Tenet was not liked, his opinions were not welcome at the Condi Rice strategic table.
Bob Woodward recounts the (unconfirmed) details of a meeting attended by Bush, Rice and Tenet where Tenet told them there was a high probability of an attack, and his advice was rejected. Knowing the strategic position of the US Administration at the time - was becoming more isolationist, leaning more to unilateral action, and that the primary advisor on National Security was not of the opinion that Islamism was a major threat to the US at the time.
As the Commander in Chief and the then-head of the NSA - the two people most responsible for US security, do you really think that either of them want it to come out that their own dogma and personal dislike of individuals was the prime factor behind the inaction prior to, and on the day?