You're very charitable to Clarke. I would characterize him as a partisan liar. The entire purpose of his testimony before the 9/11 Commission was to exonerate Clinton and place all blame on Bush. How that point of view conforms with reality is beyond me.
I don't think it's too surprising he did everything he could to cover Clinton's butt: Clinton-as far as he was concerned- was The Man; because Clinton had elevated him from mid-level staffer to near-Cabinet Officer status-and let him carry a gun as well !( To Clarke,who was perhaps the Ultimate Wannabee, that would have been a VERY big deal.)
When the Bush administration took office,they were forced to cram transitional issues into a very small space of time,and I doubt counter terrorism was at the top of the agenda - quite simply because there were too many other pressing issues to deal with.
Again, I've tried to subtract politics from the analysis.
Oddly enough, when I started looking at Clarke, it was from the standpoint of backgrounding a possible traitor- as he seemed to fit some of the profile-but he emerged as "clean". (Deluded and egotistical,but loyal.)