Secretary of Defense Robert Gates is leading the Department of Defense in a wrong and dangerous direction by cutting or killing major weapons acquisition programs, a military analyst said in an issue briefing paper.

Loren B. Thompson is chief operating officer of The Lexington Institute, a think tank near the Pentagon focusing on defense and other issues. He voiced his warnings in a paper titled “Analytic Flaws in the Emerging Gates Defense Posture.”

A major flaw in the Gates budget plan for the fiscal year ending Sept. 30, 2010, is that because the United States faces new types of threats such as terrorists and the roadside bombs they plant, the United States therefore can assume it is possible to back off preparations for major wars against near-peer competitors, Thompson asserted.

On the one hand, Thompson agrees that if — if — the total amount spent on defense doesn’t increase much, then there is “a zero sum game” where buying more items aimed at countering insurgents or blocking terrorists will necessarily mean scaling back or abandoning procurement of other types of weapons.

In his budget proposal to President Obama, which the president can accept or alter, Gates proposed slashing or jettisoning many platforms: in missile defense alone, there would be no more planes for the Airborne Laser program, no more interceptors for the Ground-based Midcourse Defense system, and no new money for the European Missile Defense system, which would coast on any funds it received in the current fiscal 2009.

Gates also would end production of the C-17 transport plane, and drop the Combat Search and Rescue helicopter, or CSAR-X, before the first helo was even built. Those all are programs of The Boeing Co. [BA].

As well, Gates would deep-six the F-22 Raptor superstealth, supersonic cruise fighter plane after 187 were built, even though the Air Force until recently said 381 were needed, and then said maybe 240 or so. It now agrees with the boss, saying that 187 will do. Air Force Secretary Michael Donley and Air Force Chief of Staff Gen. Norton Schwartz recently asked for 60 more Raptors to be built. But in an op-ed in The Washington Post today, they saluted the Gates decision to cut off production, arguing that 60 more Raptors would cost $13 billion over several years. (The total Gates defense budget plan exceeds $500 billion in fiscal 2010.)

Lockheed Martin Corp. [LMT] makes the plane, which is the most advanced fighter aircraft on the planet, a fifth generation wonder that can take out any other fighters with ease, even the best American planes.

The Gates plan, to be sure, may not become reality. A storm of outrage has erupted in Congress and among many military officers and defense analysts, who see the cuts as leading to American weakness.

Thompson is among those dismayed by the cuts, especially citing the looming F-22 termination.

While Gates said that the defense spending spigot that was turned on by the Sept. 11, 2001, attacks will now be turned off, Thompson said that is a dangerous move.

“Just because the spigot has been turned off at the Pentagon doesn’t mean the Gates spending priorities are right,” Thompson wrote.

He cites four flaws that may lurk in the Gates strategic plan for the military force defending the United States and the biggest economic powers on Earth:

Defective Forecasts. “Gates echoes the president in saying we ‘must enhance our capabilities to fight the wars we are in today and the scenarios we are most likely to face in the years ahead.’ Unfortunately, U.S. policymakers have been notoriously bad at forecasting future threats. Think of all the surprises of recent history — the attack on Pearl Harbor, North Korea’s invasion of the South, Sputnik, the Cuban missile crisis, the Tet Offensive, the collapse of communism, 9-11, etc. The record says we seldom know what’s coming next, so basing our defense posture on the belief that we do isn’t smart.”

Diminished Deterrence. “Gates clearly doubts the need for a new air-superiority fighter, since he wants to end F-22 production at a number far below any analytically- derived force objective. He also says the Air Force won’t need a new bomber anytime soon, and that the Navy can get by with only ten aircraft carriers (a level that arrives in 2012, not 2040). Isn’t it likely the reason we feel so unthreatened today by the forces of other nations is because our weapons deter aggression so effectively? So what happens when our weapons cease to impress? Other nations will respond to U.S. cuts by becoming bolder.”

Additional People. “Gates apparently believes that future threats require a more labor-intensive military posture. So the number of military and civilian personnel in the defense department will increase, while investment in technology will decline. The new mix promises to be very costly over the long run, since the government’s commitment to personnel involves pay and benefits averaging $100,000 per person per year that extend decades into the future. If you think weapons costs are up, check out military healthcare — up 144 percent in eight years! Why do we need all the new personnel if we’re getting out of Iraq?”

Exaggerated Danger. “Gates thinks the reason the services want so many sophisticated weapons is because they have an exaggerated idea of the conventional threats they will face in the future. Well what about his own assessment of unconventional threats? Do we really need to retool our whole defense posture to cope with pirates, narco- terrorists and religious zealots? After eight years of fighting a ‘global war on terror,’ the accumulated U.S. casualties are about the same as were suffered by both sides in the three-day Battle of Gettysburg in 1863 — and that’s counting the civilian losses on 9-11.”