Alright, first things first. Winter Soldier is in spirit a political thriller, it may not be of the Tom Clancy variety of political thriller but it has enough elements to it that it can be easily placed into that political/espionage category, maybe more along the lines of a lighter version of a Bourne or more recent Bond film. The undertones and themes are as plain as the nose on your face that the creative team set out to create a political/spy movie, Captain America was more or less the perfect character to fit that type of movie, possibly the only superhero character that could work in that type of movie. Just because the movie isn't as hard hitting as some spy or political movies doesn't change the intentions of the film makers.
Second, upon further analysis between the two film I've kinda discovered a surprising link in that one deals with people's reaction in the face of anarky and one deals with people's reaction in the aftermath of anarky. The Dark Knight is analogous to facing terrorism at the time it's happening, there's destruction, confusing, panic, misinformation, like real terrorism it's utter chaos, authorities are stretched to their limits and no-one is quite sure what's going to happen next. Winter Soldier is analogous to what happens in the aftermath of such terror, government overreaction and overreaching, heightened surveillance and wiretapping, fear and paranoia, government branches do whatever they can in order to obtain a sense of control over future attacks. In that sense Winter Soldier is almost a spiritual sequel to The Dark Knight.