The one aspect of the series that has been challenging with regards to modern society and politics has been S.H.I.E.L.D. - the organization that out NSA's the NSA. The organization's director, Nick Fury, is so shadowy and ethically questionable, he rides the fascism line HARD. Dealing with such a group must be a trial even for someone as strong as The Hulk.
The star spangled hero Captain America, a man left over from the WW2 generation, is especially uneasy with this group, and even more so with a world that accepts it as necessary. THIS is what he fought for?