Timothy Noah, in Slate, points out some interesting parallels between the FBI and CIA failures leading up to September 11th, and the alleged New York Times failures catalogued by Ken Auletta in the New Yorker. One parallel he didn't note, though, is that press coverage of both controversies focuses inordinately on process, rather than substance, in explaining the claimed failures. This may be a quirk of journalism; in the business world, "process-oriented", when used to describe a manager, is a euphemism for "clueless", but many journalists (including, apparently, Noah) have swallowed the fiction that management is an elaborate art/craft/science in its own right, and can be improved through technical adjustments in methodology.
For example, both the Times and the Feds are accused of operating too centralized an organization, and giving insufficient leeway to agents in the field. The infamous "Rowley memo", in which a Minneapolis agent complains that pre-September 11th investigation of Zacarias Moussaoui was blocked by FBI headquarters, is cited as evidence of too much central control at the FBI. Similarly, Auletta invokes the threatened departure of Jill Abramson, Times Washington bureau chief, as proof that editor Howell Raines is too heavy-handed with his subordinates. But highly centralized organizations are sometimes more effective than decentralized ones, and there are certainly plausible reasons for exercising considerable central control in a visible, politically sensitive institution like the FBI (or a newspaper of record like the Times). If the D.C. headquarters of the FBI was staffed with incompetents (or, for that matter, with highly competent leaders who happened to have made a single very bad call), then that says nothing about whether field agents should in general defer to their superiors or be granted more leeway. (Similarly, Jill Abramson, for all I know, might be a primadonna who could use a little "bigfooting" from Raines.)
The finger-pointing and apparent lack of coordination between the FBI and the CIA is also less clearly problematic than it might appear. Rivalries--even bitter ones--between allied organizations can be spurs to industriousness and innovation. (They can also, of course, be merely petty and destructive; what matters most is how effective each organization is, not how many rivalries it nurses.) And the FBI and CIA are, to some extent, supposed to be at odds; one mission of the FBI, after all, is hunting for moles within the CIA.
By no means am I suggesting that either the FBI or the CIA (or the Times) is a healthy organization. Their problems, though, are unlikely to be a matter of management science. Rather, large organizations fail mostly due to incompetent leaders, low-quality rank-and-file, or an obsolete, ill-chosen or ill-defined mission. With respect to the CIA and the FBI, September 11th took care of the last problem, and will likely solve the second one over time, as the agencies in question become attractive career paths for top-notch people with a patriotic bent. Whether the first problem has been solved remains to be seen; but I can predict with confidence that degree of centralization, intragovernmental rivalry, or some other pet issue of "process-oriented" managers will not determine the ultimate answer.