Overall, Ironman 2 was an enjoyable movie but it does suffer from some of the same problems a lot of these sequels do; that of introducing too many characters. I watched an interview with Jon Favreau where he realises that it is a problem but only a problem if all the new characters are pointless. And in this respect he does tackle the extra players fairly well.
The problem is that one of the best things about Ironman 1 was its simplicity and this is somewhat muddled in the sequel with these extra people.
So if I were to change things, I would agree with many here to cut Black Widow, Nick Fury and the whole SHIELD element (Maybe leave in the agent from the first film).
Also it's clear that there are influences from the 'Demon in a Bottle' story line, but it would have been better if Rhodey became War Machine to step in as a hero when Tony was going over the edge with drink, as opposed to kinda stealing the MK2 from him.
One more problem that didnt sit well with me was near the end when Tony confesses he is dying to Pepper. This scene, which was to be a really important point in their relationship, was played out over 2 monitors watched by Happy and Black Widow?! This didnt feel terribly passionate shown in the way it was and I can help but feel it was done in this way to further justify Black Widows involvement. I would be much happier to have seen this as an intimate (well as intimate as you can get while one of the people it flying a 200 mph) moment between the two, and would have really help sell their kiss at the end, which to me came a bit out of the blue.
Also, I think they missed a trick by not having Hammer/Vanko in cahoots with the Ten Rings.