[trebleshot]

With regards to Thor, he could've been pulling his punches when he fought Tony. He wasn't there to fight, he was there to find Loki. And the individual Chitauri weren't a threat to him, but their giant flying snake ships were.

Also, most of the armors that Tony had at the end of IM3 were probably half-realized thoughts, including his MK 42 (which was explicitly stated as being a prototype and shown to be twitchy throughout the film). The MK VI and VII were both destroyed during AIM's attack on his house. He was also incredibly disturbed by the events in Avengers and tinkered to keep himself from reliving those moments. Basically, he had PTSD. I think the writers tried to do as much as they could to show Tony at his weakest, both inside and out.

Having said all that, I still agree that the Extremis soldiers were overpowered. I'd have been fine with Killian having those abilities, but not all of them.