I think IM2 should have played up the whole "the sins of the father are to be laid upon the children" thing a bit stronger. They did use it well in establishing Vanko's motivation and in developing a relationship between Tony and Ivan, and in giving some emotional weight to Tony's progress, but they sort of abandoned it as soon as the element was found.
There needed to be some resolution/redemption of Howard's sin of turning his back on Vanko. My suggestion would be to have Tony learning that his father's betrayal of his partner (leading to the creation of Whiplash) used as the catalyst for his descent into alcoholism. Then, use a realization of the parallel of his own life (creating the world's fair, turning his back on Rhodey, losing his connection with Pepper) with his father's as a trigger to snap him out of the funk. Essentially, he realizes that he's not supposed to make things better with the son of the guy his father betrayed, instead, in order to win, he's supposed to not commit the same sins as his father.
The disease and death wish don't need to be there. Just have SHIELD show up in response to his drinking.
Oh, and I agree that the SHIELD presence and setting up for Avengers thing really wasn't much in IM2. Heck, in IM1, you had SHIELD constantly trying to connect with Tony, and, then, at the end, are the first group to take on Iron Monger and protect Pepper.