Jeffrey Goldberg's recent New Yorker article "The Unknown" is pitched as a piece about the C.I.A's re-evaluation of the links between Saddam and al-Qaeda.
It is that, but it's mostly an excellent primer on the processes of intelligence-gathering generally. In fact, it's one of the best pieces I've seen on that subject in a long time. Interviewees include several CIA directors, plus Donald Rumsfeld.
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I think that the decision makers are too far "above the ground", meaning that they read reports and analyses rather than experience the reality. I remember noticing in the 70's that there was essentially zero support for the Shah of Iran among the many Iranian college students in Seattle. They were either Islamists or Communists. At the time, I thought that the communists would win. But it was quite obvious to me that the Shah was doomed, having no support among these young expatriates. And I was just a young college kid, not a CIA analyst.