First off...the comedy. It felt like all they needed was Zack Galifinakis to even out the score. I like Tony's quips, but this went way over board in the comedy. Cheap, juvenile, over used and a lot of times unnecessary.
The PTSD/panic attacks. It served NO other purpose than to remind you of the Avengers. What a slap in the face. I felt it was lazy, out of place and did nothing for the plot. It kinda reminded me of Harry's amnesia from SM3.
And here's my biggest issue...the Mandarin...they RUINED the mandarin. I'm all for taking literary license with some characters, adapting them etc. but to totally humiliate the character like they did was just about as bad as taking the Joker and turning him into a clown that runs around on a unicycle at home and talks about sports with the wife. If they were going to make a joke out of the character, don't even bother. Do it right or not at all. I would have just preferred the Extremis soldiers, it wouldn't have been half bad.
Aldritch. the first moment he came on screen dressed all my wife leaned over and asked if that was guy pierce. when I acknowledged that it was she said "yup, he'll be the villain I bet...famous actor dissed at the beginning of the movie.. kinda a no brainer". He wasn't bad, and the extremis program was pretty cool.
The end battle was actually pretty cool. I liked that we finally got to see the full array of suits for once. Only problem was that it went on for too long and the ridiculous ease at which the super soldiers tore through them was kinda over done (don't even get me started about guy pierce breathing fire).
These are just some of the ones I can think off the top of my head. Even the audience I was with seemed like they were disappointed by what they saw