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Picking the people was the easy part.

President-elect Obama and his new national security team will now turn to a world full of vexing, linked problems on every continent, and tricky, early choices. From the speed of withdrawal from Iraq to the speed of investment in Afghanistan, from Kashmir to Moscow, Obama will make some of his most important choices early. Here are some of the toughest.

IRAQ

The war in Iraq, and the promise of a radically different approach to it, helped make Obama president. But he will arrive in the White House with his predecessor having already negotiated a Status of Forces Agreement providing for a timeline for withdrawal from the country, the core of Obama’s campaign promise.

The agreement “points us in the right direction,” Obama told reporters in Chicago Monday.

The most rapid pace contemplated is Obama’s campaign plan to have all American combat troops out of Iraq 16 months after he was sworn-in — that is, by May of 2010. The U.S. agreement with the Iraqi government ensures American troops will be out by the end of 2011.

“The question is how much, if at all, do you deviate from the agreement that’s been negotiated and passed in Iraq,” said Anne Marie Slaughter, the dean of Woodrow Wilson School of Public and International Affairs at Princeton. “Does that agreement supersede what President Obama said when he was candidate Obama?”

Slaughter pointed to Obama’s decision to retain the defense secretary who played a key role in negotiating the agreement as a sign that he’s likely to conform his own policy to its timeline.

But he’ll face pressure from both sides. Iraq remains a violent and unpredictable place, with suicide bombers killing at least 31 Iraqis in two attacks Monday.

And the Status of Forces Agreement likely means that as Obama takes office, American commanders will be adjusting to a new paradigm in which they shift more of the burden to Iraqi units, allowing them to take the lead and, at times, to fail in battles with insurgents. He’s likely to face intense internal debates over how involved the United State should be on a day-to-day basis, and pressure from the Iraqi government to help in some places, and step back in others.

But Obama said repeatedly during the campaign that his 16-month timeline was realistic, and many of his supporters seen no reason to dally. What’s more, the troops and materiel are needed elsewhere.

In Chicago Monday, Obama told reporters that the Status of Forces Agreement indicates that the United States is “now on a glide path to reduce our forces in Iraq.”

“The challenge for him is going to be determining the slope of that glide path,” said Shawn Brimley, a fellow at the Center for a New American Security.”

AFGHANISTAN

General James Jones, the president-elect’s National Security Advisor, drew attention recently for stating emphatically that international forces were “not winning in Afghanistan.”

Indeed, there’s a wide consensus that the situation in the country that launched the 9/11 terror attacks is a mess: The Taliban is resurgent on the ground, corruption is rampant, and opium is the national industry. Meanwhile, the multinational force patrolling the country opposing them is adrift.

“There been no unifying strategy,” said Steve Coll, president of the New America Foundation. “NATO operates its own way, every country operates its own way, the State Department and the Defense Department don’t agree.”

Part of the answer seems to be more Western troops. Obama’s advisors hope a new, pro-American mood will encourage European and other allies to send reinforcements to Afghanistan. And Obama has backed sending two or three more American brigades to the country, though the rate of that increase will be dictated by how fast Americans can leave Iraq.

Obama will also be briefed on a new Afghanistan strategy prepared by the military, the contours of which Gates outlined in a speech in Canada last week.

“All of us agree that one of our most important, and maybe the most important, objective for us in 2009 in Afghanistan is a successful election,” Gates said.

That likely means an urgent new focus on Afghanistan, to make it – at least – secure enough to hold an election at the end of next year.

But skeptics warn that Afghanistan has bled dry other occupiers, and that the U.S. should be realistic about its goals.

“Success is not going to be the creation of a secular, prosperous, and democratic Afghanistan,” said Coll, who said a new U.S. policy will likely include a massive investment in training the country’s army and police.

“That’s the ticket home – that’s the ticket to his reelection in 2012 and getting American troops out of direct action by then,” Coll said.

PAKISTAN

The potentially catastrophic aftermath of the terrorist siege in Mumbai last week could instantly jump to the top of Obama’s list of crises to deal with – depending on how India and Pakistan respond in the 50 days before he takes the oath of office.

It falls to the Bush administration – which sent Secretary of State Condoleezza Rice to the region Monday – to try to keep the two South Asian rivals from moving back to the brink of war. U.S. officials so far seem to be succeeding in persuading Pakistan to fully cooperate in tracking down those responsible for the attacks – and in restraining India from responding with provocative military gestures.

But both countries will be looking for Obama to signal how he will manage what will still be, at best, a perilously tense situation. And Obama’s options, as always in South Asia, are fraught with danger. Will he push a new and fragile Pakistani government – as he suggested in the campaign – to crack down further on terrorist groups? Will he back off the Bush administration’s increasingly aggressive use of military strikes against al-Qaeda and Taliban elements on Pakistani soil?

Even more important, given preliminary indications that the terrorist group Lashkar-e-Taiba may be implicated in the Mumbai attacks, could Washington get more involved in pushing for a negotiated settlement to the long-held grievances of India and Pakistan over the disputed Himalayan territory of Kashmir?

“In order to start to get Pakistanis to focus on the insurgent groups, you need to have them start to feel less paranoid about India, and the way to do that is to start dealing with the Kashmir issue,” said Caroline Wadhams, a national security analyst at the Center for American Progress.

“His team has talked about the need to start working on the Kashmir issue. There’s a big debate over whether the U.S. can even play a positive role in that. They will have to decide how hard they have to push that issue.”

Look for Vice President-elect Biden to play a key role on this one – he has significant and important contacts in both countries. And if Obama needs any reminding about the potential peril posed by a Kashmir-fueled conflict between the two nuclear-armed rivals, his nominee to be secretary of State should be able to attest. Hillary Clinton’s husband once called Kashmir, “the most dangerous place on earth.”

GUANTANAMO

An easier decision for Obama is one that he widely talked about during the campaign and confirmed during his recent interview with CBS’s “60 Minutes” – his intention to close the U.S. military detention center at Guantanamo Bay.

“I have said repeatedly that I intend to close Guantanamo, and I will follow through on that,” Obama said.

There is a wide bipartisan consensus that the Gitmo should be closed. And politics would be pushing Obama to make the move even if the merits of the decision were not completely compelling. Many of his initial foreign policy and national security appointments – Hillary Clinton as Secretary of State and the retention of Bob Gates at the Pentagon chief among them – have caused grumbling within Obama’s base of support on the Democratic left.

But closing Gitmo could very well open a Pandora’s Box that could overwhelm both the political and diplomatic benefits that the action would doubtless bring for the new administration.

As in – where do the roughly 250 prisoners being held at Guantanamo go?

Some could be repatriated – but that likely will mean intensive diplomacy by the young administration at a time when it is tending to a number of other foreign policy brushfires. And if some countries do accept detainees – China is one example – what kind of treatment awaits them when they return?

Furthermore, if some are kept in the U.S., as they most certainly will be, can they successfully be prosecuted, given the extreme and extraordinary circumstances surrounding their incarceration at Guantanamo?

The possibility that a future terrorist act could result from a current Guantanamo detainee being freed is truly the stuff of nightmares for the new Obama national security team.

MISSILE DEFENSE

Russian President Dmitri Medvedev put his country firmly on Obama’s agenda by attacking the president-elect the day after his election.

He and Vladimir Putin have also made a specific demand: That Obama scrap plans to set up a missile defense system based in Poland and the Czech Republic.

Obama has been a skeptic of missile defense, raising doubts primarily about whether the technology is ready. He’s also signaled that he would like to work more closely with Russia on a range of other issues, beginning with nuclear proliferation. However, he and his advisors are skeptical of Russia’s autocratic leaders.

Hawks want Obama to signal that he’s taking a tough line, and that he won’t be intimidated by Russia. Moscow would like him to put missile defense on a back burner before they arrive at the negotiating table.

Some arms control advocates see a middle ground: Obama can continue to question the system’s technical capacity, making space to negotiate.

“A decision on new deployments of strategic missile interceptors can be deferred until the system is proven effective through realistic tests and has the full support of U.S. allies,” Daryl Kimball, the president of the Arms Control Association, wrote in the Washington Times last month.

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