Shane Black definitely leaves his own imprint on the series. It's darker and scarer, but also quirkier: the quick-fire witticisms are present but they form a kind of ambient background for the real standout gags, which feel a bit like something out of Arrested Development, obsessively calling out and undercutting the conventions that structure the narrative. Black also wraps up the series in a really satisfying way: Stark finally lets go of the technology he relied on to stay alive and protect himself from the chaos around him. The film describes the suit as a 'cocoon' from which a whole Tony Stark can emerge from. Indeed, extremis (which he uses in the end to heal himself) serves as internal armour, a nice symbol that could have been developed further.
Unfortunately, Aldrich Killian is too much of a cartoon villain for this to work out. His motive is less an understandable (even sympathetic) drive for self-perfection and more a typical Dr. Doom-like resentment at the successful hero, and we've been here before with Sam Rockwell. Maya Hansen is a more ambiguous character, but doesn't have enough time to establish herself. Perhaps it would have been better to have her as the duplicitous mastermind, as she was in the Warren Ellis comic.
I still prefer Favreau's Iron Man, which maintains a clear thematic through-line and is impressively compact (apart from the robot punching at the end). Favreau was lucky in that Stark was a more interesting character back then, shifting dramatically from apathetic hedonist to troubled hero. Black is dealing with a hero fully-formed, now suffering from anxiety attacks caused by a brush with death. Even this could have been developed further, tho – just steal from Lovecraft. Stark faces down the awesome hostility of the universe and comes back fretting about how the hell the Earth can be protected. You could even add an existentialist twist: have him wondering whether his fellow human beings, trigger-happy with their nuclear weapons, are worth saving. Admittedly difficult to build up all this drama and provide a neat conclusion for the trilogy. Perhaps this stuff is being banked for when Joss Whedon puts everything together again in 2015.