Iron Man 3 was a great movie but I did feel it had some quite large flaws:
--Why didn't Tony call SHIELD? Nick Fury? Cap? Banner? Hawkeye? Black Widow? He discovers the location of the Mandarin, and rather than alerting the authorities and bringing in some super powered muscle, he goes in ALONE with MAKESHIFT weaponry he made in a garage?!?!
Granted, this is a complaint you can levy against any comic book story, but being the first post-Avengers movie, I really feel they needed to directly address this issue.
--I also thought that too much time was spent with Tony being completely cutoff from his technology and friends.
--And I also thought the AI running the suits like that stretched the semi-plausibility a little bit. Was the single Jarvis operating system running 41 different suits at once? Why not just get SHIELD agents in there?