I recently saw Iron Man for the second time, and I was reminded of why I liked it so much the first time. The science in the movie, pseudoscience though much of it is, is relevant in the sense that it both reflects current science research and shows a possible window into the future of some scientific endeavors. As such, it is a much better science fiction film than what I've come to expect from Hollywood Superhero movies.
While most if not all superhero films have to do with science in at least a nominal way (Spiderman gets bit by a gentically-modified spider; the X-men possess a "mutant gene," etc.), Iron Man is the first such film that is really about science.
In its depiction of the ability of military technology to contribute to war-mongering, it addresses the question of ethics in science research. In Iron Man's epic battles against his nemesis, Obadiah Stane, whose iron man suit is a pale imitation of Tony Stark's design, the triumph of better engineering is the theme (the first Iron Man comic book premiered in 1959, a time when, in the aftermath of Sputnik, Americans were anxious about the possibility of being outcompeted technologically by the Soviet Union). And, of course, Iron Man's suit itself is designed, initially, as a way of keeping Tony Stark alive by magnetizing shards of shrapnel away from his heart - a paean to the potential of medical technology to advance medicine and save lives. And, unlike other superheroes, Iron Man defeats his enemies not by physically overpowering them with inexplicable strength and athletic ability (see Batman, Spiderman, etc.), but by being a better scientific thinker and technician.