I never liked the idea of how the Extremis bad guy can so easily hand Iron Man's ass to him. The Extremis just takes the elements in the human body and rewrites them. It doesn't add any elements. It's an interesting idea of how basic elements could be recombined and create a deadlier species. But a human being, no matter if its basic elements are rewritten (and not added to) can suddenly dismantle Iron Man who has taken on beings such as the Hulk and Thanos.
I don't mind Tony getting beaten by a bad guy and then having to tweak his armor or technique to beat the bad guy. It makes sense. But for Tony to totally rewrite his body just to stop 1 guy is a giant leap in the pattern of what makes his character. It's having the character make a gigantic leap to get him to somewhere the writer, Warren Ellis, wanted him to be at the end of the storyline, ie a man that literally is part computer. I always felt this robbed Tony of what made him unique in the stable of superheroes. He's a normal guy (albeit with super resources) going toe-to-toe with highly-enhanced individuals.
We'll see how IM3 turns out, though. Despite my disliking Extremis as a device and my natural hatred for nano-technology in fiction (they're omnipotent in stories and can do whatever the story requires them to), I have faith in Shane Black. If Tony is using drones (potentially way too similar, even in reverse, to the end of IM2) to fight the bad guy(s), I would have preferred him to remote control his previous armors to fight Fin Fang Foom, while he himself is fighting Mandarin. Of course, it remains to be seen how IM3 unfolds.