Pierce and Stern--the latter of whom is played by comedian Garry Shandling to comedic effect--are American leaders committing wrong. But they are not presented as simply war hawks or neo-conservatives who read too much Bill Kristol. They're depicted as part of an evil conspiracy doing evil things in order to bring about world domination as enacted by a splinter cell of NAZIS who went Dr. Strangelove when inside the U.S. government.
I just do not see that as seriously dealing with it, because they are clearly evil men doing evil things who can be stopped and punished.
In The Dark Knight the questionable and immoral actions are being executed by Batman, Jim Gordon and Harvey Dent. Two of them end the film as heroes, but that does not mean what they do is right. In fact, it leaves them both bitter in TDKR and bites them in the ass in the long-run. That is a more nuanced and challenging thing to audiences, because it is purportedly good men doing morally repugnant things that might have some positive ramifications (which the WSJ's editorial page patted itself on the back for in 2008) and some very, very bad ones overall.
I am not saying Captain America has to tackle those issues to be a good movie. The Winter Soldier is a very good movie. I just think it treated its issues like window dressing. I imagine if the Russos had more freedom, Pierce would not have been depicted as Hydra. In fact, Hydra might not have even been in the movie. Then it would have been much more interesting.
