1) Tony not getting Extremis. As I'm sure most if not all of us know, Extremis was the "Giant Leap" moment for Anthony Edward Stark. You can divide his history into pre-Extremis Iron Man and post-Extremis Iron Man. Such a pivotal storyline, and not only did the movie not really push him that far forward, it took the time to hand the payoff to someone else while literally regressing Tony back to square one. Major Wasted opportunity!!!
2) Not enough Rhodey/War Machine. As people already pointed out here, the lack of War Machine actually being involved in the major fighting, especially in the final battle, was disappointing. He got the suit back from the President, but we didn't see him get involved in the battle with Killian? what was he doing, crowd control? And why was Tony so egregiously dumb he decided not to code any of the armors to respond to the only other pilot he can trust? But Mallen (I won't call him by his movie name. He was totally Mallen) could hijack the War Machine with ease?! Natasha & Fury made the point to berate Tony about the implausibility of this in spite of supposed safeguards back in the last movie, but Tony still didn't learn his lesson? Shame on him!!
3) The weird variability with which the Extremis soldiers are dispatched. How much force is needed to kill them? is it a building blowing up around them? Or is it just a repulsor through the chest, cause I thought they had a healing factor for that? The armor blowing up around Killian didn't do much beyond burn him but a weird stray shell (from where?) + repulsor blast is enough to do the trick? How were the other Extremis guys destroyed?
4) Did we forget we're part of a larger universe? where were the little Marvel Universe easter eggs to give appropriate nods or hints to the future? This isn't the comics, I don't think viewers should just take that fact for granted even if we're in Phase II now. well I guess this might mean Stark won't be involved in GotG since he destroyed the space armor in "Clean Slate".
And most egregiously and unforgivably in my book...
5) THE MOVIE INCLUDED BOTH A.I.M.
AND THE MANDARIN
, BUT NOT ONE REFERENCE TO M.O.D.O.K. ANYWHERE?!?!?!
and I searched like a mother****er all the way through. How is that possibly missed? Those of us who know the comics and remember the old cartoon, this would've been an epic geek moment! The closest we came to that was happy referring to Killian presentation as "a giant brain", but that's debatable at best, and definitely insufficient. I was thinking the dispatching of Killian was wholly insufficient, that he could still be alive, and if they wanted they could bring him back as M.O.D.O.K. somehow