Iron Man 3 is a well-crafted, exciting, and funny movie but there are some plot points that are not as obvious as they could be. Most of what follows is spoilers.
Tony didn't escape The Avengers unscathed. He is suffering from post-traumatic stress. Seeing Worm holes, aliens, and gods is more than he bargained for.
A plot thread through Iron Man 2 & 3 and the Avengers is the government's reluctance to depending on Iron Man and the Avengers. The Iron Patriot is an example of this - a super hero who reports to the President.
The theme of the movie is "empty suits". This shows up in multiple ways.
Suit #42 gets most of its air time while empty. There is the scene with Pepper where Tony is remotely operating it. This leads to the Barrel of Monkeys skydiving scene in which the armor is also operated remotely. During the entire middle of the movie, the suit is empty and recharging.
Multiple people wear armor. Tony has suit 42 assemble itself around Pepper and Aldritch Killian. Iron Patriot was worn by Rhody, Savin (impersonating Rhody) and the President.
Stark wore multiple suits but never for long. I will bet that he spent less than 5 minutes continuous airtime in any single suit of armor.
The Mandarin was essentially and empty suit. Killian realized that the explosions caused by failures of the the Extremis virus. Killian invented the idea of a terrorist to distract people from the real cause of the explosions. The Mandarin would then give some historic trivia that seemed to justify the bombing. The Mandarin's speeches sound similar enough to Ward Churchill's Chickens Coming to Roost talk and similar speeches from the far left to sound plausible.
