In addition to having really good action, Winter Soldier keeps the story grounded in typical "comic book morality" and plot.
One thing that really separates good comic movies from action schlock is the ability of the writers and directors to figure out what's at the core of the character. Now, we consider the X-Men to present a pretty solid metaphor for homophobia and racism, but that is largely due to Bryan Singer's work on the X-Men series. At the core of X-Men is this general prejudice and hatred, and tapping into that was key to making a good movie. This is the reason why X-Men 3 and the Wolverine movies just aren't as good and don't connect with audiences as well. In a similar vein, Sam Raimi's Spider-Man 2 understood that the appeal to the character was watching his life slip through his fingers for his borderline pathological obsession with being Spider-Man.
The first Captain America movie touched on this subject in the beginning, but very quickly lost its ground. Here, we see the little Steve Rogers try to take on a bully twice or maybe even three times his size. Despite the fact that he has no chance of winning, still tries to do the right thing.
The second Captain America starts off with this core element of Steve Rogers' character and wisely calls it into question. The issue is that of "preemptively striking down" threates before they become actualized, a strategy to which Steve finds himself opposed. Not only does this make for a tense movie and an interesting situation for Steve to find himself in, but brings up the larger question that the audience has to ask itself, "Is that actually the right thing to do?" Is the morality of Captain America outdated at best and dangerous at worst, risking lives by waiting until a terrorist strikes to pursue them? Or do these authorities have too much control and power over people it has deemed, without any kind of trial and based on electronic records, free to execute? Regardless of how you personally feel about this issue, and regardless of how the movie wishes to handle it, it is commendable that it even raises this question.
Either way, every movie must eventually, whether it be consciously or unconsciously, come down on one side or the other for the issues it raises. (Imagine how many slasher flicks have endorsed teenage virginity by keeping its sexually-abstaining protagonists alive while their more promiscuous friends wind up dead.) After my first viewing, I was afraid that maybe they skirted around this, but they do indeed come down on one specific side of things. Not only was this the right message to send to the audience, in my opinion, but from a film-watching experience standpoint was also the smart choice.
Again, think about those promiscuous teenagers (or, don't. Perverts.) Trying to find a middle ground here would confuse the plot of the movie. They can't say, "Hey, we're going to have sex, but use protection and we're getting married and deeply in love, so this is ok." That makes for a shitty, confusing plot. Winter Soldier brings this questions in, and definitively answers them, while still acknowledging the other side of things.