I don't think Man of Steel offered much in regards to substance, to be honest. It was the same 'With Great Power' type speeches we have heard in every superhero movie. I've personal outgrown that and it bores me. As an adult, I find the Iron Man movies to offer much more than the likes of Superman, Thor, and Captain America.
I don't think the comedy hurt Iron Man 3 at all. I appreciate a movie that doesn't insult my intelligence by teasing the death of a character we all know wasn't going to die. Of a character that most people seeing the movie didn't truly care about. I think the entire Pepper arc in that movie was stupid though and was the lone major criticism. Other than that, the movie offered a perfect blend of comedy and drama/tension.
Regarding substance, Iron Man 3 took the cake this year. It was just done in such a unique way for a superhero blockbuster. The Iron Man movies have always been more along the lines of Dr. Strangelove than The Dark Knight or Spider Man 2. The handling of international terror in the plot of IM3 was similar to the handling of nuclear war in Strangelove. A satire aimed at the summer blockbuster crowd. Iron Man 2 was the same thing with slimy industrialists, Steve Jobs esque egomania, obnoxious government figures, and sexual harassment in the workplace jokes. To me, that's much more substance than an old lady telling her son to be a 'good guy' by punching the angry goateed man-alien in the face.