I played in an Iran campaign twenty or so years ago right after our group got a copy of the RDF sourcebook; PC's were a group of Special Forces types who linked up with a pro US group of Iranian fighters. (And yes, I openly admit we were were munchkins - it was a long time ago!
The idea was to give the European GM (me) a chance to be a player, whilst one of the players GM'd an Iran campaign)
It went OK, but it was more structured than the Polish campaign we were used to...there was an chain of command that the group were supposed to observe, things were much more organised...we gave it a shot for a little while, but consenus was that everyone in the group preferred the more fluid style of campaign that we had going in Poland so we drifted back to that after a while. You said that a centralisec hain of command wasn't neccessarily a good thing and I'd abolutely agree with that....I'd say that we found working within the confines of an organised chain of command a little too stifling.
Iraq if I recall correctly was split into three factions, one backed by the US, one by the USSR, and one by France. From memory I don't think the RDF Sourcebook mentioned specific nuke targets.
Besides the US there was a brigade sized group of British forces present in theatre - one Battalion from the Parachute Regiment, two Ghurka Battalions, plus an Infantry Battalion (the King's Own Scottish Borderers). The French also had a large presence in the area, which included elements of the Foreign Legion. If you can get a hold of a copy of the RDF sourcebook it has a full order of battle for most of the forces in the area (I don't think it covers all of the Gulf Cooperative Council States' armies).
One thing I did have a hard time accepting at the time though was the presence of an Israeli Brigade in theatre. I always thought it was stretching credibility to have the Iranians accepting the US as allies, but having Israeli troops in the region allied with the Arab armies was pushing it too far for me.
As an aside, if you're thinking about running anything in that region, I'd recommend reading Sword Point, Harold Coyle's second novel; it's set against a Soviet invasion of Iran and the US response, and as well as being a good read has a couple of good ideas for scenarios in it.