I'm with the OP on this one, I left the game thoroughly unimpressed. In fact, I was downright bored. Beyond the numerous plot holes, I couldn't fathom anyone's motivations by the end.
I started getting pissed at the game when we started shooting Americans, because there was just no good reason for anyone to be shooting anyone. These idiots just walked into Dubai like it was nothing, it calls into question why nobody else did the same with maybe some medkits, or why nobody just walked out of Dubai since you can get pretty much everywhere on foot.
The Americans have absolutely zero reason to fire on the rescue team, I refuse to believe that several hundred men all went murderously insane all at once.
You gun down more legions of men before the White Phosphorus scene than you kill with it, I don't buy into the whole "we can't shoot our way in" excuse. Hell, they're three guys, if you can't shoot your way in you could always sneak around/through the camp. IIRC, I had a silencer on at least one of my weapons, it would have been trivial to cloak and dagger my way through the camp. Not only am I forced to take the lazy, dishonorable path, but I'm forced to kill the civilians. You can't progress without systematically murdering all of the soldiers, and you can't progress without taking that one last shot that melts all the civilians.
That scene calls a lot of things about your "enemy" into question as well, since it seems like the Americans were at least trying to help civilians, or something. I couldn't really engage in the scene like I was "supposed" to, since I never had any choice. The half-melted soldier that tries to ask you why, I shrugged and thought "I dunno man, don't look at me. I voted to go around. Hell, I never wanted to shoot any of you in the first place. Now, the devs wouldn't let me progress until I melted all of you. You certainly aren't going to guilt-trip me because it wasn't my decision; but I'm right there with you, this protagonist is a complete bastard."
From there it only gets worse. The Americans have endless supplies of helicopters, elite troops, and even a doom fortress, but none of that makes any damn sense. If they have all the helicopters, and hundreds of highly trained men, why the hell was it so hard for them to establish martial law, or evacuate all the citizens? Why did any of them stay, when they could have flown literally anywhere else? Why do the protagonists stay? If I remember correctly, you get into a helicopter and pull some strafing runs at one point. Why don't you just fly away? You aren't staying for the citizens, the insane army guys are a lost cause, the whole city's gone to shit, technically just knowing any/all of that completes your mission and is enough to return to base with, why would you hang around? At that point, you don't even have to turn around and walk out, you can fly back to base and make much better time.
I expected the final boss guy to bring some sort of explanation to the table, but no dice there. He was dead, or crazy, or both, and I stopped caring long before that. The "you were crazy the whole time" reveal created more questions and answered none. Not to mention, the whole thing was so tortuously drawn out I wanted to jump off a building just to make it stop. It even caps the game off with a binary choice where both choices are wrong, a la Army of Two: The 40th Day.
What I really liked about the game was the unfiltered look at what military hardware can do to a person. I'd like to see it extend even further in games, not out of some twisted gore fetish, but in order to bring a sense of weight to your actions in games. What I'd really like to see is a hybrid between SpecOps and Call of Duty 4, with the finger-wagging of the former stripped out, and the latter's improbable number of explosions scaled back a little. The result would ideally be a game in which you take a guided tour of awful, realistic war zones. The most haunting scenes are the ones that come and go without any warning, and with no interference. When you drop from a vent in Max Payne 3 and surprise a guard in a server room, he's something like the 3000th person you've killed. However, what makes that section stand out in my mind long after I stopped playing was the fact that I had to sit there and watch him die. The euphoria physics caused him to flail and attempt to get up over and over again, while his blood loss caused those attempts to slowly become more and more feeble. You can literally watch him fade away before your eyes, which was unsettling. Call of Duty 4's nuke section turned heads because it gave you that feeling of helplessness and hopelessness that until that point was alien to gamers. It certainly wasn't something that happened very often, if ever, in games until that point. In SpecOps, the white phosphorus scene wasn't the only scene that gave me pause, but the game constantly undercut itself. Every time I stopped to say "whoah", the game wrested control from me and forced me through all these setpieces where the game goes "WHOAH LOOK AT THIS, YOU ARE OBVIOUSLY A MONSTER. FEEL BAD NOW." Following those scripted scenes, the game would go right back to funneling me into giant, improbable gunfights and I'd turn my brain off again. I'd like to see a game that combines the unsettling elements of all of the above with none of the overt messaging. Good films do it all the time, they present an awful, unpleasant reality and then just leave it there. You don't need a message, you've likely already got one in your head. This isn't 300, where the point is to shout about honor and valor and then spill oceans of blood. Games with the goal of making people feel bad about war should just show war as it is. It's not fun, and it's not pretty. You can streamline the experience because it's an entertainment product, but all it really takes is just showing people the brutal reality of war to make them uncomfortable and prove a point.