I enjoyed the film but didn't love it, and I wanted to love it. Here were my issues, some valid, and others not, but still, they are mine...:
SPOILERS AHEAD
1. Iron Patriot - sure it's explained why he was rebranded and repainted, but story wise he added nothing to the plot, shy of the suit being used to whisk the president away. The first IM film set up this expectation that Rhodes was going to have a big role in the franchise and that never came to be. Also, Rhodes jumping out of the suit in a polo and jeans makes it seem like he's hanging out at home before he suits up - what airforce pilot doesn't suit up before taking off?
2. the twist - I'm actually ok with it because it worked but boy did I want to see a real fight with the Mandarin
3. the pre 2000 plot - sure it was great to see Yinsen - but typically story lines that rely on going back in time to tell a current story don't work for me - maybe I just still have a bad taste in my mouth after the revisionist exercise that was Spider-Man 3 - it feels like lazy storytelling
4. Maya Hansen - her story line and character seemed very underused - granted we didn't actually see her die so maybe she will be back and Black did say his first cut was 3 hours long so maybe she was cut out of the film significantly and maybe she's alive and will help Tony develop Extremis as his built in armor...
5. the villains - I always liked how the IM films were somewhat grounded - granted aliens from the Avengers kind of stretched it, but the villains here seemed more suited for a X-Men film (Sebastian Shaw) than an IM film
6. the kid - he wasn't bad, at all - but I just don't like kids in my franchise films (Indy, Star Wars, Superman Returns)
7. the ads - man there were so many ads in this film that were so clearly visible - hell Fios even got final cut by adding adding the tv reporter truck with a slow modem plot point, and the refurbished work garage at the end. For a film that is 3 hours long, of all the scenes cut they had to keep this crap in - as if they need the money... and everyone drives an Audi.
8. Too much man not enough Iron - sure Tony Stark is an interesting character in of himself, but the film is called Iron Man - I wanted him back in the suit - not in part of the suit at different times, not remotely controlling the suit, not an army of empty suits, not pepper in the suit - the longest period he was in the suit was after escaping the mansion attack, and he was knocked out for that ride.
9. the music - like it or not, in IM, IM2 and the Avengers Tony has been associated with classic rock, Metal to be exact - dropping the needle on some x-mas funk just seemed out of place, as did the music for the closing credits.
10. the shrapnel - to round it off into a nice top ten list... the quick glossed over montage of removing the shrapnel from his chest left me confused... first, what does this mean for the character? Is IM over? Does it mean he can simply move on? To what? It defined him as he told Banner in the Avengers - so what will this new Tony be like? And lastly, it completely unravels the entire plot of IM2 - if removing the shrapnel was that easy why bother to discover a new element, etc...
It's interesting that Marvel are so keen on distancing themselves from the Avengers franchise showing that these films can live on their own - they can, but let's not forget they spent the last six films telling us that they all live together. So what is Marvel really trying to say? I think it's that the Avengers can live without Iron Man, and not the other way around...