Some American officials say the U.S. reluctance to take the leadership role in Syria is the result of learning the wrong lessons from the Libya engagement; and indeed, the failure of the U.S. and its allies to help assure security after the fall of Moammar Gadhafi resulted in a vacuum that’s allowed radical groups to operate openly.

Egypt and Tunisia, two other North African countries that have hit rough patches after much-heralded popular revolts, also are struggling with the rise of the Salafist movement of literalist Islamists. While it’s unpopular with Republicans, analysts say, the Obama administration was correct in making overtures to the Muslim Brotherhood, the relatively more moderate Islamist group that won elections in both Egypt and Tunisia.

The administration’s willingness to talk to the democratically elected Brotherhood, whose spinoffs include the Palestinian militants of Hamas, also could play a role in reviving the Palestinian-Israeli peace process, the conflict at the root of U.S. unpopularity in the Middle East.

Mali

Obama faces perhaps an equally pressing, if quieter, challenge in Africa, headlined by the vexing crisis in Mali, where al Qaida-linked rebels firmly control two-thirds of the country – an area the size of Texas. U.S. officials agree that the situation requires outside intervention, but Washington is waiting for Africa to produce the ground troops for the effort – a process that will take months, at least, to finalize.

Tiffany Lynch, a senior Africa policy analyst at the U.S. Commission on International Religious Freedom, a bipartisan watchdog that makes policy recommendations to the U.S. government, said the Obama administration should focus not only on an immediate military solution to the crisis, but also on the human rights violations and governmental neglect that help turn marginalized groups into dangerous factions as has happened in Nigeria, Somalia and Mali.

“Until the U.S. government really takes a stand on these issues of governance, you’ll see a rise in local religious extremist groups that go on to become regional security concerns,” Lynch said.

The emergence of the Malian safe haven in a region of notoriously weak borders has spiked concerns among U.S. officials that Islamist movements are developing more sophisticated links across the continent, from Mali to Libya to Nigeria to Somalia – all of which until recently had been viewed primarily as isolated problems. Intelligence reports show that even as Somalia’s al Qaida affiliate, al Shabab, is on the verge of being vanquished militarily, its recruitment network across East Africa is growing.

Afghanistan

As he stumped for re-election, Obama reminded his audiences that he’s ending the longest war in U.S. history through a phased withdrawal that will see all U.S. combat forces out of Afghanistan by the end of 2014.

There is much, however, that remains unclear or that Obama has yet to decide. Major unknowns: how quickly the remaining 68,000 U.S. combat troops will leave and how many will remain to train and advise the Afghan army and to conduct operations against al Qaida and allied groups based in Pakistan. His new administration also will have to negotiate an accord with Kabul governing the status of any remaining U.S. forces. That could prove difficult.