First, I completely agree that reasonable people can come to different conclusions based on the same data. As a member of the so-called "intelligence" profession, differing conclusions come with the territory.

That said, here's my take on that paragraph:

Perhaps the greatest defect of Air Force leaders in recent times has been their failure to adapt to the changing demands of a transformed global security environment.
Where is the evidence? And what's "recent" - especially since the example given is Vietnam. As I've mentioned elsewhere, the AF reorganized in 1992 and got rid of Strategic Air Command which was the AF's most important arm during the cold war. Given the decline in nuclear security and accountability that led to these firings (which I think were necessary, btw), one might argue that the AF changed too much in that case. I personally think the AF has been more adaptable in recent times than the other services - or at least the Navy, which is where I have direct experience. When I first joined the AF after the Navy, it was frankly refreshing to be in a service relatively free of cultural baggage and what some of us Navy guys jokingly called "tradition before innovation."

Regardless, my sense is that the entire nation is still grappling with the "transformed global security environment" and what that means with respect to US interests and military doctrine and capabilities. The author doesn't give us her definition, so it's impossible to ultimately tell if her criticism is valid in a specific context.

However, U.S. defeat in Vietnam signaled that the source of danger was shifting to elusive, unconventional aggressors, and the Air Force failed to change as fast as the threat did.
I would agree with you that the sentence is basically correct, but it is deceptive by what it leaves out. Why not replace Air Force in that sentence with any of the other services or the DoD as whole? It hardly seems fair to lay blame for failure to adapt to threats posed by "elusive, unconventional aggressors" when those threats are largely ground-based and the Army didn't seem too interested in addressing them either until OEF/OIF. The AF has been pretty consistent in adapting to threats in its domain, IMO.

Finally, while it's probably beyond the scope of the article, there's no suggestion as to what the AF should have done better, much less whether it would have been possible to convince OSD and Congress to sign on to changes the AF should have taken. Nor is it clear if the AF is currently on the right track, though the author's use of the past tense might indicate that it is.

The bit about the location of the Air Force Academy and service school is particularly obtuse - one wonders if she makes the same argument with regard to Leavenworth?

I do agree with this paragraph, however, which is a very close second to the one I identified above:

One symptom of this cultural insularity is a widespread political obtuseness within the Air Force that leads it to misjudge what power brokers outside the service want or will support. For example, during the Bush years the service has expended considerable political capital in resisting the efforts of civilian leaders to buy more B-2 bombers, increase spending on space systems, and accelerate the development of unmanned surveillance aircraft. If it had simply said "yes" in each case and conserved its capital for the really hard fights like keeping the F-22 fighter in production, the Air Force today would have a bigger budget, better capabilities, and more goodwill among senior policymakers. By refusing to deal with the political system on its own terms, the Air Force has handed other services with superior political skills control of the entire joint command structure.