I think the registration will be changed to suit the MCU. For one, I think Stark has some major demons after everything he has been through. That puts him in a place where he doesn't trust other people as much. He didn't want the rest of the Avengers in on the Ultron project, aside from Banner who he needed. So the Civil War might have something to do with the Avengers being more closely monitored, and all the other heroes/villains at large. You have to take into account that Captain America: Civil War is really Avengers 2.5, so it will feature a bunch of the heroes already around plus many more. Off the top of my head Black Panther and Spiderman have been name dropped. Black Panther might be in an Ambassador role, therefore not in suit. Ant-Man is probably going to be a secret hero, come to think of it he could play Spiderman's role to a certain extent - the hero with a family to protect that will be harmed if their identities are exposed.
I see Sokovia bringing the Avengers to light in the wrong way. Already Sokovia had it out for them. They hated the shit out of the Iron Legion. Add one more major event like that, probably something similar to the Stamford Incident, and the governments will be raising hell over "enhanced" people; Calling for the Hulk to be arrested or contained, and the others as well. The Civil War in the comics ended up pitting one team of Avengers on the run against a government sanctioned one. Shield had Stark tech troops dubbed "capekillers" so they basically had power armor to fly around in.
So far Baron Zemo and Crossbones have been confirmed, so I am curious if anything to do with Thunderbolts will ever be brought up, certainly they want people to think Cap is going to die, and Bucky is going to replace him. Speaking of which, Cap will be looking for Bucky, especially with Falcon on his trail after AoU. Crossbones will have it out for Cap and Falcon big time.
Ultimately we might end up with something like Avengers Academy (New Avengers Facility at the end of AoU), where government sanctioned heroes are trained, payed, and monitored. Really this has been eluded to to some extent on Agents of Shield, where ever since the first episode they have always cataloged and registered any person with powers, placing them in a database, etc..
We might not get anything like Civil War, aside from a few nods here and there unless...lets' say they don't waste Michael Douglas's character and we still have Pym in the story. Then the only thing they really are missing, aside from a shitload of heroes, is Reed Richards who can have a stand in. So we have all the enhanced people introduced on AoS and the Netflix show's like Daredevil, eventually Luke Cage, Jessica Jones, and Iron Fist to work with. Further theorizing here, we might not get a full resolution of the storyline in the one film. We have no idea what Avengers: Infinity War will be like, especially being split in two parts, maybe the Civil War will still be going on. Oh and don't forget Spiderman will be getting a Marvel Studios sanctioned solo flick soon too.
It should be said that Thor will be gone in Asgard dealing with Ragnarok, so he will probably be out of the picture for Civil War, not unlike the actual comic. I think with the devastation heroes have brought to the world the governments/World Council will crack down hard. Shield might rise from the ashes (they have been active on the show in secret) and become a horrible enemy for the heroes to fear, at least the ones who don't want to go along with the "Initiative". Once again, in the comics, Nick Fury was on the run, with Shield in charge by Maria Hill at one point, and Tony Stark at another. Fury recruited his own team on the side. I'm curious if they might do the same.
Basically, it's too early to tell.
