While the Civil War comic book by Mark Millar and Steve McNiven was centered primarily on the idea of secret identities, the movie Captain America: Civil War will shift focus more to government control and accountability. It's a distinction that's fairly obvious, since few characters in the Marvel Cinematic Universe even have secret identities to begin with. There's Ant-Man and... presumably Spider-Man?
But even without secret identities, there could have been a Registration Act, the idea that anyone who wants to be a superhero needs to register, be trained by, and overseen by the government. That apparently is out, as well, in favor of "Accords" across the world, according to a new report by BirthMoviesDeath. With S.H.I.E.L.D. publicly destroyed (no one in the MCU knows about Coulson's team of remnants), the heroes of the MCU are seen as completely without any oversight, and thus without any consequence.
So, in this case, we'll see Iron Man and his team saying that the Government should have a say in how the Avengers operate, and they should answer to the elected leaders of the world. Captain America and his team will say, instead, that the Avengers can't be beholden to governments because it's too limiting in how they'll be able to do good. The divide is mostly between Tony and Steve, of course, as Tony wants to protect the world and accept responsibility for what he's done wrong, and Steve saw how too much oversight in S.H.I.E.L.D. led to corruption that could have been catastrophic in both loss of life and the global landscape in general.
So no, it won't be about secret identities, but then no one really thought it would be, did they? It will be about government oversight and how much freedom should be allowed to those claiming they're here to protect us - which all sounds awfully poignant in the current political landscape.