As US President Barack Obama gears up to begin a second term, his Middle East agenda will be more complex and potentially more consuming and dangerous than the one he inherited from his predecessor four years ago.

Back then, the pressing priorities were: winding down the US military presence in Iraq; pursuing an Israeli-Palestinian peace; rebuilding America’s damaged image and frayed relationships across the region; confronting violent extremism; reining in Iran’s nuclear ambitions.

Today, the US military is out of Iraq and a recent Zogby Research poll shows that, after a dip in 2011, there has been a marked improvement in the approval ratings given to the US across much of the region. That, however, is the only good news. The rest of the story is deeply troubling owing, in large part, to the unsettling effects of the crumbling of the region’s old order.

While the US is limited in its ability to manage the fallout of the Arab Spring, the Obama administration continues to believe that it is in the US’ interests to assist, where it can, and to seek to mitigate, where possible, the hardships or the violence that has flowed from these largely internal developments.

The bottom line is that Washington will have its hands full in the Middle East in the coming years. What follows is a snapshot of the problems the US will face.

Egypt: because of its size, position, and cultural and political leadership role, Egypt remains a key player in the Arab world. When Egypt had its “Arab Spring” moment, the impact on the entire region was profound. If anything has been made clear by the events of the past few weeks, however, it is that the revolutionary process that is reshaping Egypt is far from over. It appears that the Muslim Brotherhood has overreached, seeking not only to win elections, but also to use its victory to monopolise power and silence opponents. This has caused a backlash that has further destabilised the country.

The US has some economic leverage here and is attempting to maintain a balance between respecting Egypt’s fledgling democracy while insisting that the Morsi government protect political freedoms and work to compromise with its opposition. How this will play out is far from certain, but Egypt and the success of its democracy will remain a concern.

Israeli-Palestinian peace: the rights of Palestinians, always at the core of Arab and regional concerns, will of necessity continue to be front and centre on the administration’s agenda.

It will be there because Palestinians continue to insist that their rights be recognised, because the rightwards drift in Israeli politics continues to lead to policies which inflame tensions, and because US credibility is tied up with how it deals with this issue that continues to evoke such deep passion across the Arab world.

Syria: The situation in Syria goes from bad to worse. The Assad government continues the bloody assault on its people as it is confronted by an increasingly radicalised and militarised opposition that has taken hold in several parts of the country. US and allied efforts to fuse together a broader political opposition have been somewhat successful, but serious questions remain about the ability of this grouping to control, or even relate to, armed elements operating throughout the country. Syrians remain deeply divided, with growing fears that there will be sectarian bloodletting — like the one that occurred during Lebanon’s “long war” or during the US occupation of Iraq.

There are voices in the US, and the region, calling for giving more arms to the opposition or the establishment of a “no-fly zone”, or other forms of intervention. But none of these proposals addresses the “day after” questions.

Given this, the nightmare of Syria will either drag on for the foreseeable future, will be resolved by the collapse of the regime, or, at best, by a messy negotiated compromise leading to a transitional government. But whatever scenario plays out, the Syrian “Pandora’s box” has been opened and will not close anytime soon.

Syria’s fallout: already the fallout from Syria is being felt region wide. There are heightened sectarian and ethnic tensions in Lebanon, Turkey and Iraq, and vulnerable Jordan has been impacted as well. Kurds in Syria are demanding independence and being aided by compatriots in neighbouring countries. In other areas, Sunni/Shiite tensions have been exacerbated, and Christians in Syria and region wide are feeling threatened. Add to this, the looming humanitarian crisis caused by the increasing influx of refugees and the tragedy of Syria promises to be a major concern that will consume the administration for years to come.

Iran: pressure continues from Israel’s friends in Washington and from several Arab Gulf states for the administration to deal with Iran’s nuclear programme. Should the president make a renewed overture to engage with Iran, it is hoped that the Islamic Republic will respond wisely. It would also be smart for Washington to take a page from its approach to North Korea and to include Arab allies in the conversation, not sideline them as it did in the past.

No one should have an interest in a military confrontation. Neither the US nor the countries in the region will benefit from the crisis that would ensue. Should that occur, the issues facing the administration and the region will only become more complicated and more out of control than they are at present. But there should be no doubt that pressure will continue and tough choices will have to be made to resolve the issue of Iran’s programme.

If all this were not enough, there are still fires burning in other areas that will continue to require attention. Iraq’s political situation remains quite tense and could easily flare-up in renewed violence. Libya is still largely out of control, with armed militias operating beyond the control of the country’s newly elected government. Bahrain’s sectarian tensions are still simmering and unresolved.

And despite the death of Osama Bin Laden, extremist groups, far from defeated, have metastasised into diverse regional threats taking root in several conflict zones.

And so, before pundits and policy makers glibly speak of US policy “pivoting East”, as if the Middle East were an “old story” with which we are finished, it is important to understand that the challenges the region presents remain serious and, despite our limited influence to direct outcomes, they will continue to require attention in the coming years. Thus begins Obama’s administration second term.