Probably because those changes weren't played for laughs. I would have been fine with the twist, of the Mandarin being nothing more than a front, if they didn't turn it into another joke, in a long list of jokes. I mean seriously,
this is what we got?
Then add in the fact that the marketing for the movie showed the exact opposite. That wasn't a twist as much as it was a misleading lie.
If you tell me we're going to get ice cream and show me ads in the paper for Cold Stone all week then ultimately take me to WalMart and buy me a Great Value brand ice cream sandwich for a nickle, that's misleading. Or as I'd call it, cinematic entrapment.
That being said, my answer to the poll, I'd have to say Iron Man 3 by a small margin over Iron Man 2. All of the films had their issues (Thor had a ton of cheese, CATFA had inconsistency in their effort scene-to-scene, TIH seemed hollow at times, etc.), but Iron Man 2 and 3 had the most problems. And Iron Man 3 gave us bigger expectations and had a few more, let's call them "insulting" moments to the viewers.
The Mandarin thing, no need to elaborate.
Not enough Iron Man.
Too many corny jokes that didn't fit.
Too many "now why would _____ even do that to begin with?" moments.
The "PTSD" issue was VERY poorly done. And the solution to it was even worse.
The destruction of the armors was pointless.
They moved from plausible villains to unrealistic villains.
Tony remotely controlling the Mark XLVII during the Air Force One rescue had no risk to Tony himself (and where did the headset come from?).
Pepper gaining powers and killing another villain.
They teased about the background issue with the Vice President, but didn't follow it through, leaving it to feel empty and added on last minute.
Even the post credit scene, while funny, was unfulfilling.