As we know, the plot for [Captain America: Civil War](tag:994409) is that Iron Man and Captain America are on opposing sides over a registration act put up against superheroes to work for the government doing what they say.
We believe we know why Tony is for this act after all the destruction he has done after creating Ultron. He probably believes this is the best and most logical solution. But now then why is Cap against it? We believe it is because of the events of Captain America: The Winter Soldier, with S.H.I.E.L.D turning out to be Hydra, he would be hesitant to trust the government again that quickly but in Avengers: Age Of Ultron:
S.H.I.E.L.D comes to the rescue by evacuating the city and Cap says to Quicksilver that is what S.H.I.E.L.D is supposed to be. And then at the end of the film the New recruits for the New Avengers that Cap is leading is run by/with S.H.I.E.L.D
Which makes it hard to believe that it's just the events from The Winter Soldier that make him go against the government. That makes me believe that Agent Coulson is the reason for Cap's defiance.
Agent Coulson, arguably everyone's favourite S.H.I.E.L.D agent and Captain America's biggest fan. Coulson was the most important character in The Avengers because his death gave The Avengers something to Avenge and was for Cap emotional Guilt for letting his number 1 fan down.
So to find out that Coulson isn't actually dead anymore and that no one has actually told him after 3 almost 4 years could be the final straw for Cap. After having doubts following the events of The Winter Soldier. Of trusting the government he still believes S.H.I.E.L.D is a great concept for hope but with the reveal they have been hiding another secret from him and a very personal one at that he decides S.H.I.E.L.D should not be allowed to control the heroes. The possibility of this is happening is becoming more and more likely because of the way Agents of S.H.I.E.L.D season 3 is going with the introduction of Inhumans on TV. And them randomly appearing over the world the movies can't ignore that so a crossover isn't unlikely anymore.