Captain America is a product of science and as is the Winter Soldier. They are both designed to help the war propaganda backed by different ideologies. Though the execution changes from comics to movies, essence remains the same. 
 The science behind Captain America has grace, a degree of dignity in the way the serum is designed to work. It embodies Rodger's own values, his ideals and general good intentions. He is a simple guy in a very complex world where the distinction between black and white is blurry and in some cases doesn't even exist. Yet, he sorts through the mess and arrives at semblance of right and wrong. Maybe the ideals of the 40s was best suited for captain when the world was, well, less self-absorbed. 
 The winter soldier is a weapon, designed to shape the world. The steps taken to make him the ghost he is, are extreme. He becomes the perfect soldier in his own regard, following commands the way it is expected out of him. 
 In this way they are both the same. While Captain America indeed has his own choices, these choices are influenced by the information he has in his hand. There is a point (in the movie its quite blatant) where Rodgers wonders about the authenticity of the information he has been given. Brubaker explores the contrasting nature of the two sides slowly and allows the readers to derive their own conclusion. There is enough material here to question hypocrisy of SHIELD's decision. 
 [The art work was surprisingly mediocre. Captain America looks weird when there is supposed to be some emotion on his face. I kept seeing Chris Evans though!]