Gates is a paradox in another sense: A self-described protector of institutions, he has also, in less than four years on the job, changed the way the Pentagon does business and the military fights wars more than any defense secretary since Robert McNamara.

But there’s a haunting dimension to this comparison. In his first two-and-a-half years running the Pentagon for President John F. Kennedy, McNamara brought rational analysis to weapons procurement and shifted military planning from “massive retaliation” (with an emphasis on nuclear bombs) to “flexible response” (and a buildup of conventional defenses in Europe). Yet this side of his tenure is completely overshadowed by the disaster in Vietnam.

Only somewhat less dramatically, Gates has heralded a shift in military planning from the “major combat operations” anticipated in the Cold War to the “asymmetrical conflicts” against insurgents and rogue states that plague the 21st-century world. Yet Gates, too, understands that his legacy will be shaped much more by the outcome of the wars in Afghanistan and Iraq — wars that he did not initiate, and occasionally had doubts about continuing, but which he now undoubtedly and unhesitantly owns…

Gates, who turns 67 in September, says he wants to leave the job and retire, this time for good, sometime in 2011. “I think that it would be a mistake to wait until January 2012,” he said. It might be hard to find a good person to take the job so late, with just one year to go in the president’s current term. And, he added, “This is not the kind of job you want to fill in the spring of an election year.”