The other night I was watching Batman Begins for the umpteenth time when I had an epiphany. The Batman and Iron Man trilogy has one very important plot point in common, and based on Captain America: The First Avenger the other two Captain America movies may have a similar pattern.
The plot point I speak of is that in Batman Begins, Iron Man, and Captain America: The First Avenger, the titular characters all are born to fight an evil organization led by their worst enemies. For Batman there's Ra's al Ghul and the League of Shadows, who first trained Bruce Wayne, but then became his worst enemy once he realized that they wanted to destroy Gotham. Then there's Tony Stark who was captured by the terrorist organization known as the Ten Rings led at the time by Raza, who may have just been a figurehead working for the Mandarin. Finally, there's the Red Skull and HYDRA, who is the primary reason that Steve signed up for the Super-Soldier program and became Captain America.
Now in those three movies Batman, Iron Man, and Captain America seemed to have destroyed those three organizations after defeating the villains who led them. Therefore, in Iron Man 2 and The Dark Knight those organizations were nowhere to be seen as Batman and Iron Man took on Joker and Whiplash respectively, who had no ties to the Ten Rings or the League of Shadows, but were their own brand of monster. I have a feeling that even though it is speculated that Alexander Pierce is the Red Skull or Baron Zemo in disguise this will not be revealed until the post-credits scene. This would then make the Winter Soldier his own monster, and those working with him seem like rogue SHIELD agents.
Finally, there's The Dark Knight Rises and Iron Man 3. In these two movies the Ten Rings and the League of Shadows came back to battle Batman and Iron Man in an even bigger way. Also this time there were fresh faces to lead those two organizations in the forms of Bane and Trevor Slattery/the Mandarin. I believe that in Captain America 3 the plot will be similar with HYDRA coming out of the ashes of the seemingly destroyed SHIELD as a bigger threat to Captain America than they were in the 1940s. Also if TDKR and Iron Man 3 are any indication there will be a new leader of HYDRA either in the form of Baron Zemo, or possibly Baron Strucker will return after his appearance in Avenger: Age of Ultron. However, if Alexander Pierce is not already Baron Zemo then I believe that his leadership will be temporary because he will have only been a figurehead for the returned Red Skull. Now it is my hope that the Red Skull, Baron Strucker, and Baron Zemo each lead their own army of HYDRA soldiers as they invade different areas around the globe in order to try and start World War III. This would lead to an epic final battle, and a epic grand finale for the Captain America trilogy if this is where Marvel decides to end this series. A battle like this could possibly be so huge that other Avengers members like Hulk or Iron Man or Quicksilver or Scarlet Witch could get involved as well.
I know this theory may sound crazy to some and sane to others. Feel free to either tell me off or agree with me in the comments section below.