|This is why we can't have nice things|
The US invasion in 2003 overthrew the Sunni leadership under their strongman Saddam Hussein, and the rush to something that looked like 'democracy' led to elections without any other established democratic institutions, resulting in the expected 'tyranny of the majority', and the inevitable Shi'ite state. This allowed a sudden sea change, the theocratic and political alignment of longtime enemies Iran and Iraq. With Iraq's infrastructure destroyed by years of war, their economy in tatters and their society fragmented, it was left for Iran to step in and provide assistance and guidance to the allied Shi'ite Iraqi leadership in Baghdad.
The US Response:
The US claims that Iran is a key adversary and one of the greatest threats to peace and security in the region, while their major regional ally, Iraq, is a US ally. That creates the situation where the US is allied with Shi'a Iraq (but not with their benefactor, Shi'a Iran) against Sunni IS, and is therefore tacitly allied with Iran in the war against Islamic State.
Syria's leadership is Alawite, which is a branch of Shi'a Islam, and their primary opposition is, predictably enough, Sunni. IS, al Quaeda and even the Free Syrian Army, to whatever extent that was ever a real organization, all were Sunni groups arrayed against the Alawite leadership. A leadership supported, predictably, by Iran, and opposed, every bit as predictably, by Saudi Arabia.
The US Response:
The US is opposed to the al-Assad regime, and has aligned itself against the Damascus/Tehran alliance that, with Russian support, has kept the regime in power, albeit with a dramatically reduced territorial footprint. Therefore, in the Syrian conflict, the US is supporting the Sunni insurgents in the battle against the regime loyalists. At the same time, when the US flies airstrikes against IS positions in Syria, they are tacitly supporting the Shi'ites in power ind Damascus, despite rhetoric claiming exactly the opposite. This kind of supporting-both-sides tactical incoherence serves only to extend the conflict.
Houthis, a Shi'ite splinter similar to the Syrian Alawites, overthrew the Sunni government of Abd Rabbuh Mansur Hadi in Yemen, bringing them into conflict with Sunni extremist fighters in and creating another potential Syrian style conflict, where the sectarian divide becomes inextricably tied to the political, and there is no path to solve the disagreements but an endless fight to the death.
The US Response:
The US has been actively fighting to support President Hadi, a Sunni, in his fight to survive the Houthi insurgency, with the full spectrum of drones, SpecOps, weapons and training. Now that the Houthis have succeeded in deposing the Hadi government, the Houthis are working to consolidate their power, while the opposition Sunnis, led by al Quaeda fighters resist them from their enclave in Aden. Yemen is on the brink of civil war, and the problem for the Houthis is that long border with Saudi Arabia. If the Saudis decide to actively support the Sunni resistance - which is highly likely - they will be working to hand Sana'a over to what would essentially be an al-Quaeda (or IS) led government. US troops and drones have been withdrawn for now - will the US support the Houthis on the Saudi border or will they continue to support Hadi's fight to retake the Presidency, despite the fact that his primary fighting force is composed of al-Quaeda jihadists? Judging from history, the US will claim to be supporting some kind of moderate, inclusive government based on some kind of nonexistent moderate Sunni power structure. Meanwhile, the Sunni resistance will become exclusively jihadist in its makeup and it will become impossible for the West to support.
None of the forgoing should suggest that any of this is easy. Regional political and diplomatic goals often find different champions, and the nature of the risk should define the nature of the response. But that's precisely where the US is so wrong-headed about the current sectarian conflicts throughout the region. There is nothing inherent in either side - Sunni or Shi'ite - that could convince the American leadership to focus its support on one or the other. They are both violent, bigoted, misogynist, 7th century throwbacks that do not seem to be able to live together in peace, or even provide for their own people. As long as the arguments can't be worked out by systemic political and territorial compromise, as long as they are at least partially premised on events of over a thousand years ago - events that may or may not have even happened - as long as someone's family name or method of worship marks them for summary execution, there are no 'good guys' and there is no faction worthy of external support.
The US should be entirely neutral in these conflicts. We should offer to mediate, and even provide troops and resources to implement and support a peace agreement. But the American leadership should be very clear that until the shooting stops we will not be a party to what is essentially a sectarian conflict. That American blood and treasure should be spent over ancient mythological hatreds is bad enough, but to support both sides almost at random only guarantees that the conflict cannot end. Endless war should not be an American foreign policy goal.