I kept expecting to hear the villain say, "Just as I killed your father!" He never did, which was good.
The biggest plot-hole I thought I spotted - why would Stark Industries do business with a small pack of terrorists? - was actually a plot point. So huzzah.
Most of the rest of the things that bugged me could be explained by Tony Stark being Tony Stark. Helmets during testing? Padded test area? Test area that's away from my expensive cars? Pssh! I'm Tony Stark, what could go wrong?
That Jervis / the house / the robot arms' capabilities expanded or contracted to fit the scene is somewhat to be expected. (Tony: You can program the robots to get you into and out of your suit, but not to swap out your pacemaker? And Jervis doesn't have 911 on speed-dial? Dude.)
Best line: "So how did you solve the icing problem?" Delivered in the exact tone used by researchers everywhere when confronting colleagues with a mixture of real curiosity, sneaking jealousy, and/or the hunch that the other guy isn't all that, after all.
But most awesome thing about the movie: The HRI/HCI (human/robot and human/computer interface). The head's up displays looked too fussy (the audience is expected to be stunned by them, not actually get information off of them) but the natural language interface with the robot arm, the 3D drafting/simulation/development environments, the smart house, all the tools Stark had at his disposal: their technologist/futurist earned his bread there.
Moreover, the movie did not suck. There were no plot holes you could drive a truck through, the actors were engaging, the dialogue was overall good. I notoriously cannot "turn off" my brain during a movie, so if I can't find things to nitpick, it is a Good Thing.
More seriously: The movie opens, but never really addresses, the moral issue of weapons manufacture and research. Over on the bad side, we have selling advanced weapons to bullies (whose motives for decimating villages isn't really explained - what was their tactical plan there?). Over on the good side, we have the US Armed Forces, who aren't given any dark agendas in this movie. (Probably tellingly, the military action takes place in Afghanistan, a much less contentious engagement than Iraq.) The Manhattan Project is referenced at least twice, but colored differently each time. The first time, it's held up as a triumph, the thing that ended WWII and prevented an invasion of Japan. The second time, it implies the dawn of the nuclear age, the Cold War, and all that followed.
It was, of course, both those things.
The movie's message is ambiguous: Stark uses the Iron Man suit to stop terrorists and blow up their weapons caches - oh, and kill them. The suit is a weapon, no mistake, and it's meant to be frightening when the villain has his own version of it. But Stark doesn't destroy his own suit in the name of peace. In fact, he's making another one. Because of the good he can do with it. (And in good mythic American vigilante style, while he's willing to entrust it to a particular airman, he won't build it for the Air Force.)
Maybe that's as much clarity as one can get on the issue.