I can't tell if some of these posts are jokes or not. I am trying to be helpful but what other insight do you think forum members can give? How can we give better judgement on your application than the director of the program?
I don't think you need any ego stroking from anyone here, you are clearly a highly qualified applicant.
When you are rejected by the schools, they automatically send you that template email without further soliciting, and I dont think they would cry and feel sorry as you are now haha
I would highly consider Georgetown, especially since you're looking at government service. Georgetown's programs sometimes get a bad rap in the academic world as being too "policy" (I'm political science now but serious considered MES). It would give you a lot of flexibility and if you can defer, you have the opportunity to do Fulbright AND look for outside grants to get you a bit of funding.
Chicago's Near East Studies department is very much NOT modern, but there Mid East Center definitely has more of a modern feel. (And Lisa Wedeen does a TON of work on Syria so that might really be of interest to you.)
As for Harvard, I think you should talk to some students in the master's program. Sometimes PhD students have a hard time getting prof time (so I've heard...may be untrue). Getting some perspective from current students would probably help your decision.
Good luck! (I lived in Jordan for awhile, and ABSOLUTELY loved it.)