I didn't mind the twist, but a couple other things bothered me:

Pepper Potts, even with Extremis, flipping around and defeating an Iron Man armor. FAIL. I laughed out loud actually.

It bothers me that SHIELD and the Avengers did not even have a throw away line to explain where they were for this. I mean, Stark disappears and they don't show them helping? Not even a mention, for a terrorist organization threatening the US president. I know the comic books do this all the time, but this is based in reality, and it irked me.