Afghanistan—Either we stand by our commitment to Afghani rebels or we forget about it altogether and let the Soviets choke on it. American nation-building in Afghanistan in 1989 would have been a humanitarian measure that would have prevented much ugliness both in Afghanistan and elsewhere.
Iran—We should never have blindly supported Shah Pehlavi. Seven presidents—from Franklin Roosevelt to Jimmy Carter—were kind to the Shah. The Carter administration was the first to notice this, but by then it was far too late to pressure the Pehlavi government for any reforms. We could have done better there much sooner, probably after World War II, or before 1960, at the latest.
Further, if you step in and address the hindsight question after the fall of Pehlavi’s government, it’s safe to say we should never have sold Iran anything in the way of arms. (However, that was more of a domestic criminal issue than a foreign policy one.)
Palestine and Israel—“The bride is beautiful, but she is already married,” said a prominent Jewish pundit in 1947, foreseeing problems in the near future for the planned Jewish state in the Transjordan. Perhaps it would have been better not to have created a new state in a place where an ethnic group was already living (a.k.a. colonization), but the United States should have pushed for a recognized Palestinian state there, as well. (Granted, I also hold Great Britain accountable for the shortsighted mess in Palestine.) Two nations with Jerusalem as an open city and fixed borders for both would have solved many, many problems. Again: hindsight.
Turkey and Iraq—The United States should have stuck it out in the League of Nations and pushed for a separate Kurdish state to be carved out of the old Ottoman Empire. A separate Armenian state would have been just, too, though this would have been difficult, with the newly-formed Soviet Russia running the bulk of Armenia. Otherwise, Turkish borders are just fine.
Iraq—The United States should never have supported Saddam Hussein. Just because he was “our thug” didn’t justify supporting him. Had we not built him up, the (justified) Gulf War would never have happened.
Nejd, Hejaz, Asir, Aden, Oman, the UAE, Qatar, Bahrain, Kuwait, Iraq, Transjordan—In exchange for military support in World War I, Great Britain promised Sharif Hussein that they would support a Greater Arabia of sorts. Hussein took Britain up on it, made trouble for the Ottomans, but got shafted in the end. Saudi Arabia became a major force in the divided Arab world, which was just beginning to govern itself for the first time in centuries. The colonial powers—Britain, France, Italy and Spain, mostly—kept the Arab world fractured. I guess this wasn’t exactly something you could pin on the Americans, though a more forceful stance for Sharif Hussein back then would certainly helped our standing now, whether Hussein succeeded or not. Ideally, Europe and the United States should have allowed this Greater Arabia (or whatever it would have been called) to form, then pressured it to move toward a democratic government. That plan still may not have worked, but I think it would have put our hearts in the right place.
Pakistan—Simply put: stand by your friends. Sure, the Cold War’s over, but we should have stuck by Pakistan’s side. We owed them that much.