President Obama may think he played it smart by choosing CIA Director Leon Panetta to replace Defense Secretary Robert Gates and Afghanistan commander Gen. David Petraeus to take Panetta’s job at CIA. Both men have superb reputations and each is a shoo-in for confirmation.

What comes after won’t be so easy. Both Panetta and Petraeus are being air-dropped into unfamiliar roles at a time when the agencies they’re taking over are under enormous stress both politically and substantively.

Gen. Petraeus has, for the past decade, been one of our nation’s principal intelligence consumers. He has had to make decisions in Iraq and Afghanistan on the basis of a dearth of actionable intelligence. By now he knows in detail the major weaknesses of our intelligence community, and especially the CIA, in penetrating adversary nations and non-state actors such as al Qaeda and Hezbollah.

Now he’s going to have to look through the other end of the telescope, and what he’ll see isn’t pretty.

As Petraeus will discover quickly, the CIA has more fractious tribes than Iraq, each with its own political agenda and media/congressional constituency. It is encumbered with a supervisory bureaucracy that adds no value (the Director of National Intelligence) and has suffered so many attacks from congressional Democrats that Petraeus’ predecessor, Panetta, was forced to spend so much of his time defending the agency that the mission of the CIA — to gather intelligence — was further eroded.

Because it was unable to gather essential intelligence, under Panetta the CIA turned to its “lethal authorities,” the employment of paramilitary operatives and its own fleet of Predator (and other) unmanned aircraft. These assets have been engaged in a global game of “whack-a-mole.” Though they have managed to kill a great many terrorists and some minor terrorist leaders, they have not succeeded in crippling — for example — the three major terror networks in Afghanistan, al Qaeda, the Taliban, and the Haqqani network in Afghanistan and Pakistan.

Before he can get to those issues, Petraeus will face the first challenge encountered by every retiring military officer (or senior industry executive) taking a high-ranking civilian position in government. When a general or a CEO gives an order, his subordinates — if they don’t want to get fired — move out smartly to accomplish it. In the civilian side of government, when the boss issues an order, it’s the start of a debate, not the end of one.

(I e-mailed a friend of mine who works for General Petraeus asking if he’d be coming to Langley with the boss. His answer was, “DC is too much of a war zone for me. MUCH safer here in Afghanistan.”)

When the general enters his new office, he will discover proofs of what he suspects. We are unable to obtain reliable current information about the sources of the greatest threats our nation faces. Iran is a “denied area” in which we have almost no ability to gather intelligence. China is embarked on the most penetrating espionage effort against us since the Soviet era and terrorists are still able to hide, obtain financing and weapons, and mount attacks against the U.S. and its troops abroad with too great a frequency. The attempts by the Christmas Day airline bomber and the Times Square car bomber failed only because of their ineptness, not our measures to interdict them.

Petraeus undoubtedly has a lot of ideas on how to improve the CIA’s gathering and analysis of intelligence. And he will try to implement them, only to have the CIA’s tribal culture and its congressional/media supporters thwart him. He won’t get the active presidential support necessary to reform the intelligence community because Obama has himself been at war with the CIA, alleging in his 2008 campaign that it tortured terrorist detainees. Obama backed Eric Holder’s 2009 appointment of a special prosecutor to investigate torture allegations. That special prosecutor’s work continues to this day, a doomsday cloud still hanging over the agency.

Whether Obama is re-elected or not Petraeus will, like James Woolsey before him, probably leave in frustration after a short term at CIA.

Petraeus will be frustrated at CIA. But what is politically worse for Obama, Panetta’s term as defense secretary will be disputatious and rocky from the start.

Panetta — former House Budget Committee chairman, White House Budget Director and Clinton Chief of Staff before coming to CIA — has been picked because his political credentials seem to make him a good candidate to wield Obama’s machete in slashing the defense budget. But during his term at CIA, his relationship with many senior House Democrats was poisoned by their unremitting attacks on the CIA over the issue of terrorist interrogations.

House Speaker Nancy Pelosi’s war on our spies never ended. As ranking Dem on the House Intelligence Committee, Pelosi was briefed on September 4, 2002 on the fact that al Qaeda detainee Abu Zubayda had been waterboarded, but denied it repeatedly. When the Director of National Intelligence released an unclassified summary of the briefings (a story I broke on May 7, 2009), Pelosi accused the CIA of lying.

Panetta, to his credit, stuck up for the agency he headed, releasing a statement on May 15, 2009 that the CIA’s policy was to not mislead Congress. Eleven days later, Pelosi and six other House Dems sent him a letter demanding that he recant that statement.

Relations between Panetta and congressional Dems sank to such a bad level that, in an unprecedented August 2, 2009 op-ed in the Washington Post, Panetta wrote, “It is worth remembering that the CIA implements presidential decisions; we do not make them. Yet my agency continues to pay a price for enduring disputes over policies that no longer exist. Those conflicts fuel a climate of suspicion and partisanship on Capitol Hill that our intelligence officers — and our country — would be better off without. My goal as director is to do everything I can to build the kind of dialogue and trust with Congress that is essential to our intelligence mission.”

Whatever ill will still exists between Panetta and congressional Democrats, Republicans won’t march to his support when he tries to sell $800 billion in cuts to the defense budget over the next decade, as Obama wants. House Armed Services Committee Chairman Howard “Buck” McKeon is very dubious about the cuts made by Obama and Robert Gates, and isn’t going to go along with the additional cuts Panetta will try to sell.

Panetta will also have to confront the soured relationship between our professional military and the White House. Not only is there a problem with distrust of the president over Libya, the repeal of “Don’t Ask, Don’t Tell” and a host of other issues, National Security Adviser Tom Donilon is distrusted by many of our military leaders. When Donilon was being considered for the post, according to a Bob Woodward book, then-National Security Adviser Gen. Jim Jones said that Donilon had no credibility with the military.

It’s understandable why Obama would pick Petraeus and Panetta for their new roles. But the dangers our nation faces will not — cannot — be solved by these men. The problems they face aren’t made insoluble by the terrorist groups and nations that mean us harm. The obstacle to solving them is the president they serve.