Whether that ignorance came from inept investigation, the reliance on predetermined assumptions, or something more sinister may never get answered, unless Congress holds their creation responsible in public hearings for these oversights. The sudden discovery of the trove of data left out of the Commission's report and apparently their deliberations clearly shows that the report and its conclusions can only be called incomplete in the most charitable interpretation of events.
As Hayes points out, the problem with the charitable interpretation is that it ignores a certain pattern of "ignorance". The Commission appears to have included every data point that supports the popular notion (even before their start) that the 9/11 attacks came with almost no state support other than the Taliban in Afghanistan, and even then only in sheltering the al-Qaeda strategists who ordered the attacks. The "dots" that the Commission excluded from even a mention -- if only just to debunk them -- all seem to point to state assistance from either Iran, Iraq, or both. Most of them show that the intelligence community actually did uncover some interesting data, on which the bureaucracy either explicitly blocked further investigation or discouraged action. Why would the Commission want to do that? Could it be that the collection of bureaucrats that comprised the panel wanted to believe that the bureacracy could save America, and that the intelligence communities needed more constraints, post-9/11? Or could they have wanted to underscore the meme, during a presidential election, that our "unilateral" approach to policy regarding the two potential state actors had no basis in national-security requirements?
ShrinkWrapped first called them the "9/11 Omission", and the name is becoming more appropriate every day.