After careful thought about the twist I have come to the conclusion that... you're wrong. In the first movie Iron Man's enemy was a military industrialist who employed a group of terrorist to help him sell more weaponry, in the second film it was a military industrialist who employed a single terrorist to help him sell more weaponry and in the third... a military industrialist who manufactures a terrorist to help him sell more weaponry. How exactly is this a step forward since it seems that Iron Man is just fighting the same guy in a different suit. In all of the movies it's just a rehash of military industrial complex: bad, Iron Man: good.
By nerfing the Mandarin they actually lost the opportunity to get deeper into the moral questions that are inherent to Iron Man as a whole. Stark Industries does not produce weapons. Unless they are for Stark himself in which case it's okay for him to make a missile that can take out a tank and is only the size of a cigar. You can barely own a handgun in California, which has some of the strictest gun laws in the US, but he has more than 40 high powered, advanced weapon systems in his basement and no one bats and eyelash. How does he get away with that? He is involved with a super secret organization that can conduct military operations anywhere in the world and can even order a nuclear strike on a major American city and no one knows who they answer to. The Mandarin could have been the guy to call him on this. He could have raised the questions of how much of a danger to the rest of the world does Iron Man represent. Americans might think it's cool to have an Iron Man who is an American but would the rest of the world agree? Would any other country or population feel threatened by the fact that he can just go into whatever country he chooses and start toppling governments just because he doesn't like what they're doing based on what he saw on CNN? Instead we got "military industrial complex: bad, Iron Man: good".
What I really liked about the twist is how it worked with the terrorism angle.
It was all smoke and mirrors, and the fear was in our heads.
Just like real terrorism, it's the idea that makes it real, even if the Mandarin wasn't.