Feige confirms that Iron Man 3 will adress the events from Whedon's Avengers:
"So much of the journey of 'Iron Man 3' is informed by Tony's experiences in 'The Avengers. It's almost like post-traumatic stress: he really has retreated after the events of 'The Avengers' into his workshop, where he's building advanced versions of his suits. He has [designed] a version of the suit that can latch onto him in individual pieces ... anytime, anywhere. As he starts to realize, it's basically because he doesn't want to be out of the suit: he's seen a lot of things in 'Avengers' and has encountered a lot of powerful people, much more powerful than he is."
As we've seen in the trailer though, Tony will not be able to hide in his home for long, as it is destroyed, along with his workshop and armors. But Feige says it pushes Tony forward and in a way, back to his beginning:
It brings us back to the Tony we met in the first part of 'Iron Man' where he's removed from that convoy and brought to the cave with nothing but a box of scraps. It's fun for all of us to watch Tony try to figure out how to get out of that scenario. Much of the movie is Tony in the middle of the country without his tools and a fairly broken suit to help him. But that's his superpower: he wasn't born on Asgard, he wasn't hit by gamma rays, and he doesn't have the super soldier serum. His power is his brain. It's fun to put Tony Stark in a corner with nothing and see how he can get out of it.
Feige also addresses the direction they've taken with Iron Man's villain: The Mandarin, in the movie:
We felt there was leeway to explore the Mandarin in a way that hasn't been explored before. We found we couldn't point to any sort of definitive Mandarin story in the comics — but if you print this, I'm sure a million fans will point to a specific story — so as we've done with many of the films, we did an amalgamation. The Mandarin is relentless: he's a non-stop threat, and you've seen that in the first teaser trailer when Tony Stark's house tumbles into the sea. He doesn't mess around, this guy.
He tells MTV that director Shane Black, and all the cast really, put their all into the movie. Adding that Shane had "worked in the shadows" of the first Iron Man film, but this would definitely be "his Iron Man". And that they haven't worked much out for the next Iron Man movie, as they plan to focus on Avengers 2 next. Right now, Tony has enough to focus on with overcoming what he went through in the Avengers and finding a way to defeat the Mandarin without his Armors or lab.