In terms of plot. I think Killians whole plan was plain brilliant and great social commentary. That's just me though. And yes I know, I'm in the minority. I love IM3. It's not a perfect film but I do feel like is hate is way overblown. I believe it's genuinely a good film. Though the 3rd act needed to be polished a bit. It was basically a video game.
I liked the Mandarin bait-and-switch, and the use of Killian.
My quibbles with the movies were;
1) Did not like the music. The first two had a sort of AC/DC classic rock vibe, and with IM3, they went somewhere very different.
2) Did not like the Extremis inventor dying like a chump (I just created something that makes a person pretty much unkillable, and I'm working for a dude who shoots people for no reason at all! Let's *NOT* make myself hard to kill...). The MCU could certainly use an interesting female antagonist, and one that Stark inadvertently created by dismissing her all those years ago would have been a fun poke.
Still, if someone really wanted to, they could film a 30 second scene of her getting up, glowing red, the bullet hole closing up, and muttering, 'Idiot.' and wandering off to begin her new life after Killain 'killed' her.
3) Did not like how at the very end they tried to wrap everything up with a bow. I destroy all my armors (except the destruct command mysteriously doesn't affect the Iron Patriot armor, which would have killed Rhodey and the President, so, uh, lucky me the auto-destruct on that one suit of armor malfunctioned)! I get rid of the arc reactor keeping me alive, 'cause apparently I don't need it anymore! I cure Pepper, so she can't possibly go on to become a neat super-character in her own right!
It was written like this would be the last time we would see Stark or Pepper again. (And in Pepper's case, that might be true.) We already knew that Downey was signed for more movies, and would be in Age of Ultron, Civil War, and / or Infinity War, so the whole 'I blow up my armors and remove the arc reactor that powers them!' nonsense was obviously a big fat fakeout. In the theater, I was wondering why they were even writing this as some sort of ending, when it clearly wasn't.