Religion
I know people love to contribute their atheist views on nearly every thread, but that's a terrible example.
Religion, and, I don't argue it's trueness since that's not what this thread is for, but, possibly due to people liking it in history, has done some good on this planet people just occasionally tend to forget.
Other problems, though, such as poverty, war itself, lack of tolerance, etc, have done nothing but good at all.
If you want counter examples -- then you should know that one core argument that Atheism uses to contradict Christianity is their belief in the Old Testament or respect of it, which they say is flooded with offensive suggestions/warlike ones. At the same time, you chose to say the Middle East is low and violent. Why is your view not the same for the Christian World? Furthermore, Islam in itself isn't as Middle Eastern as everyone thinks, culture has embedded itself much more like a rock than the religion itself has, and that being said, the middle east is low and violent due to it's lack of unity following the disbandment of the Ottoman Empire and lack of control over their own governments and national resources.
Furthermore, the Crusades bought about an end to the European dark ages and helped spread knowledge across into Europe, which eventually lead to some remarkable inventions for mankind.
The inquisition, though obviously lacking tolerance, did help to re-unite Europe as a 'Christian' Nation, which, I think in a way, helped to begin the trend of creating nation states. Though it was a terrible act, the idea of still having empires and territorial possessions over war sounds much worse to me.
Furthermore, in feudal Europe, Churches were a place to find education, not to kill people. Albeit, it is understandable that all that you learned within the church wasn't all tolerated at the same level, that still does not disprove their significance in actually helping people.
Now it's possible to argue that if religion weren't around history would have fun different courses, but that is simply not the case, nor is it the case today. So it doesn't make sense to call it the world's biggest problem that we have to get rid of. Just my thoughts.
Personally, I still think poverty wins. It's the root source of many issues. Also, sometimes, the end result of many others.