All the side bits about the Darfur 3 saga go here. I've already got it written; just need to do a LOT of cut and paste.
Eastern Afghanistan, 2001: I chose this area due to the international nature of the war. The UNSC, with China and Russia having veto power, would not want the US deploying superhumans to 'minor' wars like the NATO action in Libya. I chose the battle of Tora Bora since the Air Force was active in that battle and the introductory character, Karyn Allwyn, was in the Air Force.
Darfur and South Sudan 2007: I chose this area due to the nature of the world alliances involved in the conflict. The United States would not request superhumans from their country to fight there, since Sudan allies Russia and China would vote NO. But... if the rebel groups have superhumans in their armies, the US trainers get to train them. After all, it's not THEIR army, and rebel groups are not members of the UN. This is where the Darfur 3 come in...
Helena, MT, USA: I loved seeing pictures of 'Big Sky Country' when I was a kid and from what I remember of the X-men's many institutes, I wanted to combine the two into one place. I had three reasons for this.
1) In-story, I made a joke about the 'Calcutta Cringe', an incident in the early 90s which involved a person in Calcutta. He was trying to learn how to use his vibration and sonic powers. Unfortunately, he discovered 'the brown note' and EVERYONE within 4 miles crapped themselves at the same time. After that, you could imagine world governments coming up with creative ways to help supers and keep them out of city limits while training.
2) I was partially inspired by many cartoons and comedy shows growing up in regards to this situation. Let's face the facts- people are not going to tolerate teenager/adult superhumans wrecking infrastructure while training. You're not going to be in a happy mood if some garisly dressed kid crashes through your bedroom window because he doesn't know how to fly.
3) The area west of Helena has lots of rugged mountains and hardly any people. Perfect place for super fights, and a perfect local economic booster. I threw in a couple of conversations involving the characters and the locals as one would expect in 2012.
Aso, Ada, Belsalji, Nuland: These places are far away from civilian populations, which make great places for superhero training or secret government bases. That's the optimistic answer. The real answer is that governments can nuke those areas in case the super trainees go berserk, whereas nuking a large city might enrage the populace.