As he prepares to leave the Pentagon after a four-and-a-half-year stint as defense secretary, Robert Gates has been making the rounds to his old stomping grounds, delivering farewell addresses designed to make his audiences squirm.

He did it again today, before the American Enterprise Institute, the think tank that, as he put it, has been “inextricably tied to the war in Iraq, the conflict that pulled me out of private life and back into the public arena” (a move about which Gates clearly feels both honored and ambivalent).

His message to the assembled neocons was this: Like it or not, the defense budget is going to be cut over the next 10 years; he’s already weeded out the particularly wasteful or redundant weapons systems and bureaucratic structures; so we’re going to have to slice into “force structure”—Army divisions, Marine expeditionary units, Air Force wings, Navy ships—the meat and muscle of U.S. fighting power.

Rather than take the easy way out and “salami slice” a certain percentage of all costs off the top, a technique sure to leave a “hollowed-out” force (plenty of troops and weapons but too little money for operations, maintenance, or training), Gates said the Congress, the president, and the American people must make conscious choices of what military missions to forgo and what level of risk to accept.

It’s a good point, and I think it’s also Gates’ way of saying that he’s relieved to be leaving this job—not just for all the reasons that he’s mentioned or implied already (he’s tired, he’s been at this for longer than he’d intended, he hates Washington, he yearns to retire to his two nice houses in the Pacific Northwest), but also because he’s reached the end of his comfort zone when it comes to slashing the defense budget.

In both halves of his tenure, the last two years of George W. Bush’s presidency and the first two and a half of Barack Obama’s, Gates has been a transformative defense secretary—more so than any since Robert McNamara under President John F. Kennedy. (Under Lyndon B. Johnson, he slid into tragedy.)

Gates killed or halted more than 30 weapons systems, including some of the services’ most cherished chestnuts (the Air Force’s F-22 fighter, the Army’s Future Combat Systems vehicle, the Navy’s DDG-1000 destroyer). He forced the chiefs to build or accelerate a new generation of weapons that rubbed up against their institutional interests but were vitally necessary to the wars they were fighting (the MRAP, mine-resistant ambush-protected, troop-carrier and a slew of unmanned aerial vehicles, aka “drones”).

He has helped change the military culture: the way the Pentagon does business and the services fight wars. But he has no interest in challenging that culture’s foundations—the global reach of U.S. military power and presence. That is to say, he’s a radical, to the extent that he has forced the bureaucracy to perform its missions more effectively—but he’s a conservative, in that he’s dedicated above all to preserving those missions.

President Obama wants to cut defense spending by another $400 billion over the next 12 years. A coalition of liberal doves and deficit hawks may force deeper cuts still. The Simpson-Bowles deficit-reduction commission, for instance, recommends cutting it by $1.2 trillion. Gates probably isn’t the ideal man to do that; he won’t be around to do it anyway; all he’s saying, with one foot out the door, is that his successors should at least do it sensibly.

There was a time when the Defense Department and its overseers in the congressional armed services committees did this sort of analysis routinely. But the knack, or the demand for it, dried up during “the post-9/11 decade,” when the military grew “accustomed,” as Gates put it in his AEI speech, to a “no-questions-asked” attitude on funding requests for anything and everything the services wanted. Adm. Mike Mullen, chairman of the Joint Chiefs of Staff, made the same point in hearings this past January: “We’ve lost our ability to prioritize, make hard decisions, make trades.”

The question is whether Congress will just slash money arbitrarily, the salami-slicing that Gates fears, or whether it—and the team that Gates’ presumptive successor, Leon Panetta, puts together—will restore the art of military-budget analysis.

Gates did a fair bit of this in his time. He halted the F-22 not just because it was an expensive Cold War relic but because his analysts noticed that the Air Force’s justification for continuing to build more planes was deeply flawed.

At the time, the Air Force already had 183 of these planes. Its senior officers wanted to build a total of 387. Yet their case for this expansion, laid out in internal briefing books, assumed that the United States would someday fight two wars simultaneously against two foes with just as much air power as we have. It also assumed that a large percentage of the F-22s would be in routine maintenance depots when the wars started—i.e., that the two foes would coordinate a surprise attack.

The unstated implication was that if the attacks did not come as a surprise, and if we therefore had more of the F-22s online and ready to go, we wouldn’t need quite so many planes to begin with. And if we were willing to let go of the premise that two comparably powerful nations (a resurgent Russia and a much more powerful China?) would go to war against us simultaneously, the 183 F-22s that we already had—in addition to the many other planes in the arsenal—would be plenty.

And so Gates stopped the project. Obama agreed, to the point where he announced he would veto the entire defense bill if it contained money for a single additional F-22. And Congress went along (with 15 Republican senators joining in), despite the fact that the Air Force had over the years ingeniously parceled out contracts and subcontracts to corporations in 44 states.

Many other weapons systems and military missions could be subjected to the same sort of analysis. For instance, the defense budget that Obama and Gates put forth in February includes $24.6 billion for 11 new ships, $4 billion for two new Virginia-class submarines, and $1 billion for a down payment on a new nuclear aircraft carrier. Are all these things really needed? What are the assumptions and scenarios that support the case? How valid are they? Do we need to spend $9.4 billion to buy 32 F-35 stealth fighter planes, when we’re also spending $2 billion to upgrade the older (but still world-class) F-15s? And what about the $1.4 billion for 24 new Trident II submarine-launched ballistic missiles? Is our nuclear deterrent degraded without them?

These are the questions that Gates is saying we need to ask, even if he might disagree with the answers.