With the talk of how Cap 3's title is somehow immediately significant, it occurs to me that a Captain America: Civil War movie, in one form or another, makes to much sense and has too much potential to not be a possibility. One would think it would have to be dramatically different to funciton--after all, there are hardly enough heroes for them to go to "war" against each other, and nobody seems to have secret identities anyway to go to war over--but when you think about it, a lot of the pieces are already there.
Civil War wasn't really about identities, it was about regulation--some low-rent superpeople screwed up, a school was blown up, and the government finally did the obvious thing and decided there needed to be regulations to manage all the superpeople running around.
You can find seeds for this idea in Iron Man 2, where some legitmate questions are asked about why we allow a wealthy drunk in a wearable fighter jet to drop into the middle east and start blowing people away. Avengers takes the idea further by having SHIELD creating contingencies against Hulk and Thor.
The final piece is in Winter Soldier, where we see Captain America become disillusioned with SHIELD (for very specific reasons, sure, but disillusioned all the same), and Nick Fury (the Avengers number one proponent in the government) is taken out of the picture.
All it takes now is for an Avengers wannabe to cause a tragic accident, and suddenly we have the setting for Civil War--but not a war between heroes: a war between the heroes and SHIELD.
Now, the idea would have to be massaged--you have to give SHIELD sufficient reason to arrest the Avengers, and you have to give the Avengers a reason to fight rather than cooperate--but these are details that can be worked out. The most significant difficulty is that it would be hard to do the idea justice without having it take over Avengers 3. You can start with Cap 3, but if you have a war between SHIELD and the Avengers it's likely to spill into Avengers 3. It's a drastically different direction than Thanos, so that's tough to pull off.
That said, somehow, at some point, I think this is an idea that can work--and has too much potential not to explore, especially with a SHIUELD show on TV that can show us the SHIELD side of the argument and have us sympathize with both sides.