Civil War wasn't about secret identities, it was about HAVING to work for the government. Go where they say when they say it. That's how the MCU will play it. Tony will side with the registration as a sign of penance for the creation of Ultron. Cap, who has seen what happens when you put everything under one umbrella, sides against. I assume that the NEW Avengers (Cap, Vision, the twins, Black Widow, Falcon and maybe War Machine) will all be on the anti-registration side. Tony, Bruce and Fury will be pro-registration I'm assuming. Bruce and Tony will be driven by their penitence. This storyline will supposedly carry over into Avengers 3, followed by the arrival of Thanos in 4. Remember, 3 and 4 might film back-to-back and be released roughly a year apart.