There's various stupid stuff in the movie, most of which I just ignored as comic-bookisms. A few forced me to throw brown penalty flags. The pretended impotence of the US government relative to Tony Stark was annoying enough to get a post of its own. Linear accelerators do not get adjusted with monkey wrenches. There are undiscovered elements out there. They're undiscovered because they break down faster than anyone can find them. This keeps them from being an OSHA-friendly replacement for whatever you'd been using.
A more subtle technical complaint: if you're making armored drones there's no point in making them bipedal. Tanks are shaped the way they are for a reason. You want to take advantage of the cube-square law--the less surface area you have the thicker the armor can be.
Tony and Pepper really aren't going to have a decent relationship until they're in the habit of being honest with each other. So, never.
Of all the high tech wonders shown in the movie the one I want the most is the augmented reality social display. Arrive somewhere and it automatically highlights the most important people and displays their identity and key data about them. Oh, yes, please. Heck, I'd settle for one with a "What's your name again?" button that'll pull it up on request.
All the fussing over whether Tony should have a monopoly of the Iron Man suits does involve a real issue: who can be trusted with that kind of power? The movie is a good argument against entrusting it to mentally unbalanced alcoholics. I know a fair number of people who wouldn't be happy with the US government having it. But once the genie is out of the bottle, what do you do with it?
This debate happened before with nuclear weapons. Heinlein tackled it with the stories "Solution Unsatisfactory," "The Long Watch," and Space Cadet. His method relied on recruiting people with the moral fiber to choose suicide over wealth and power to stick with their principles. I think the first title holds true. celticdragonfly came up with some ways to make that system more reliable. I pointed out she'd recreated the Guardians from Plato's Republic. She pointed out we were probably the only people who watched a superhero movie and wound up referencing Plato. Best practical possibility we came up with was a carefully recruited order of Catholic monks. Which would, of course, be the Brothers of St. Michael.
I completely agree with Howard Taylor about what Tony should be doing with his reactor.