So I have heard a lot of f and on about how Civil War (Which I tend to agree) is a bad story arch for a movie. I agree it was a bad story arch. I disagree that it is a bad movie choice.
It obviously will not be entirely about hero registration/Secret Identities. Mainly because there are barely any heroes around in the MCU that have secret identities. Meaning that this is a pointless issue.
If anything I suspect it will be about the same thing Captain America spoke against in Winter Soldier regarding Big Brother government oversight.
We already know (Spoilers) that Stark has been name dropped regarding picking up the Security torch SHIELD dropped when Hydra was exposed.
It is also a given fact Stark as he put it in Avengers... Has all of SHIELD's secrets.
It is a given fact that Stark and his character flaws would be a poor choice for someone to be in charge of such a thing, especially considering his actions against terrorism in Iron Man 3.
Stark is a control freak in enough ways to make him a poor choice for this. Stark is much like Fury, a strike first kind of guy. Where as Rogers is a let us see people do wrong before condemning them of wrong mentality.
Stark will no doubt have a huge part to play in a technological stand point. Perhaps some form of dare I say it... Mandroid armor? A thing he originally fought against his technology becoming, only to change his tone in light of events.
I also suspect that this will be part of the rift in ideology that they had in Avengers 1 and it will be expanded upon in Avengers Age of Ultron.
Only to come to a head in Civil War.