The bad guy is terrorism. It's a story about a guy who is just trying to fix some of the awful mistakes that he made. It's low key and focuses on character growth and relationships rather than just trying to set itself up for the "next installment".

And I think they backpedalled on that growth in the second and third movies -- Iron man became a caricature and got more annoying as more movies came out (AOE and CW especially).

It was widely considered the best superhero movie at the time, that is until Dark Knight came out a few months later.