Among President Obama’s greatest national security challenges has been deciding who will replace Defense Secretary Robert Gates, as the widely popular Pentagon chief prepares to leave his post this summer.

Coming to that decision has involved a delicate confluence of considerations. Who is suitably steeped in defense policy matters? Who will have credibility both with the White House and within the halls of the Pentagon? And equally important, how will a new Defense secretary affect the balance of power within Mr. Obama’s cabinet?

The withdrawal of US troops from Afghanistan, scheduled to begin this summer, has no doubt factored into the deliberations about a defense chief. That official, and the entire national security team, will also have to grapple with the continued US presence in Iraq, the nuclear ambitions of Iran, and something closer to home: the difficult decisions that the Pentagon leader will have to make about the defense budget.

The White House has confirmed that on Thursday Obama will name Leon Panetta, currently director of the Central Intelligence Agency, as the next Defense secretary. And Gen. David Petraeus, now the top US commander in Afghanistan, will take Mr. Panetta’s place at the CIA.

It remains to be seen whether Panetta, like Secretary Gates himself, will align closely with Secretary of State Hillary Rodham Clinton in defense policy debates, or with Vice President Joe Biden, who has lobbied hard to step up the pace of the departure of US troops from Afghanistan.

As it stands now, Gates and Secretary Clinton are “an extraordinarily powerful team,” says retired Army Lt. Col. John Nagl, who heads the Center for a New American Security, a Washington think tank that has served as a recruiting ground for the Obama administration. “They’re very pragmatic, and they’ve gained strength from reinforcing each other and from developing what appears to be a very genuine rapport.”

This rapport was not necessarily Obama’s chief aim when he assembled his cabinet. He subscribed to a philosophy that involved facilitating debate “by bringing people together who weren’t likely to agree with each other, and didn’t have much of a relationship with him,” says Stephen Biddle, an adviser to senior military officials including Petraeus and a defense policy analyst at the Council on Foreign Relations in Washington. “In the next round, he may want to bring in people he has had more of a relationship with.”

This could, in turn, portend policy changes. “The power narrative of this administration on security issues has been an alliance between Clinton and Gates against the vice president and the national security adviser,” Dr. Biddle says. “From what I can tell, neither of the camps has ever persuaded the other of its views, and neither one has made much effort at breaking into the other’s fortress. What you get is a series of compromised stalemates.”

More shifts are in store for Obama’s national security team. The current term of Adm. Mike Mullen, chairman of the Joint Chiefs of Staff, ends later this year. He is widely expected to be replaced by Gen. James Cartwright, the vice chairman of the Joint Chiefs.

On Thursday, Obama will also announce a new ambassador to Afghanistan: veteran diplomat Ryan Crocker.

For now, the role of the next Defense secretary looms largest. Someone more closely aligned with Mr. Biden, analysts point out, could conceivably spur a renewed push for a speedier withdrawal from Afghanistan. Panetta is a longtime friend of Biden, with whom he served in Congress, and they have a history of supporting each other in White House power struggles.

During his time at the CIA, Panetta has intensified drone strikes against insurgents in Pakistan – an approach that Biden, too, has supported.

Still, in Afghanistan, it’s another matter whether a stepped-up US troop withdrawal makes political sense. Currently, the US public is relatively quiet on the issue, Biddle points out. Polls that find the pubic generally supports bringing troops home also find that those people “aren’t paying that much attention to the war,” he says.

Quicken the pace of US troop withdrawals, and the GOP has new ammunition. “It runs the risk of changing the politics of the war,” says Biddle. “The controversy level could increase radically – and Republicans could decide it’s a chance to attack the president as soft on terrorism.” Staying the course in Afghanistan, then, seems a prudent move going into the 2012 election season, he adds.

News of the expected nominations was greeted with skepticism in some circles. Sen. Dianne Feinstein (D) of California, for example, questioned the choice of Petraeus (who will retire from the military before assuming the CIA post). The general is more a “consumer” of intelligence than a producer, she argued. A White House official disputed this characterization, saying he was deeply steeped in intelligence matters.

In any event, his move is widely seen as a bid to bring further national security credibility to the administration. “Petraeus as CIA director brings complete fluency to the war in Afghanistan,” Dr. Nagl says.

Petraeus is likely to support Biden’s push for an advisory and counterterrorism-focused mission in Afghanistan – eventually. “Petraeus would argue that conditions on the ground need to be set first – from the insurgency being diminished and the Afghan security forces being strengthened” before the US military can do more advising and less fighting, Nagl says.

Ultimately, however, the new Defense secretary’s agenda is likely to be driven less by wars half a world away and more by budget matters – a key concern for voters.

Panetta’s experience as former director of the Office of Management and Budget is likely to be “his single most important skill set,” Nagl says. “It’s hard to imagine someone better for the job on paper.”

Momentum has been gathering to make considerable reductions in the defense budget. “If Gates has cut away the fat” from much of military spending, “then increasingly we’re cutting away at muscle,” says Andrew Krepinevich, president for the Center for Strategic and Budgetary Assessment in Washington.

Yet the pressure for cuts comes at a time when security challenges are increasing, analysts like Dr. Krepinevich argue. The challenge for the White House will be thinking strategically about which priorities can be trimmed – and which cannot.

China, for example, “is engaged in a military buildup trying to shift the military balance” in the Pacific, says Krepinevich. “Are we going to be a counterbalance?”

Secretary of the Navy Ray Mabus, who had been considered a possibility for the Defense secretary job, cited China on Wednesday as one of the most underestimated threats that the US military faces.

Also, the protests throughout the Middle East could mean changes in US relations. “Turkey, some former strong Arab allies like Egypt, and even Saudi Arabia are beginning to question their relationship with the United States,” Krepinevich says.

Iraq, too, remains an area of concern for the Pentagon – particularly if the Iraqi government requests that 20,000 US troops stay in the country after December, when all US troops there are slated to return home.

Moreover, Iran continues to pursue its nuclear ambitions.

These myriad pressures will keep building – and stress the Obama administration, Krepinevich says.

“Traditionally, when we’ve drawn down our military budget, it’s been at the end of wars,” he says. The current national security challenges are likely to mean that the “world will be a more dangerous place at the end of this decade than it is now.”

Obama’s team will also have challenges prioritizing national security issues amid economic strains. So the president may decide when he appoints the new Defense secretary, “ ‘Enough of this cabinet of rivals,’ ” says Biddle. That would probably lead to “less debate and more decision.”