Theres been a fair bit of back and forth on the question of whether Avengers 3 should be Civil War or not. This is me trying to give the question the answer it deserves by going through some comparisons between the Civil War comic, and what we know of the Marvel Cinematic Universe.
Civil War had a huge cast that involved more or less every superpowered being on American soil at the time of the event. Hundreds of named characters clashed against each other on the subject of the superhero registration act. The movie universe currently counts about a tenth of that... if we include villains... and the superheroes/villains of future Phase 3 movies prior to Avengers 3. Basically, what I'm saying is that it would be a very small, concentrated civil war, kind of like the fight between Iron Man, Captain America and Thor in the Avengers when they were trying to determine who would get custody of Loki.
Speaking of Thor, he was spending a year dead (for tax reasons) at the time of the Marvel Civil War. Try to get him to register, and that might turn into a diplomatic nightmare with Asgard. Also, Hulk was doing his own thing at the time at his very own planet. And Scarlet Witch was missing and deemed responsible for the murder of Hawkeye (who had later been resurrected, but was still outside of the action while hiding out incognito at Doctor Stranges place), Scott Lang (Ant-Man) and Vision (not to say the entire mutant race, most of whom she had recently depowered). Quicksilver was running around at human speed in the former New York mutant district desperately trying to kill a twelve year old girl (and failing miserably). To put it gently, most of the current roster of Movie Marvel Heroes were having a bad day, and weren't involved in the original event. Of the key players of the event, only Iron Man and Captain America are actually active in the movieverse. Heck, even SHIELD is down for the count (though that's likely to change).
Avengers 3 - The Story (SPOILER WARNING!)
The original Civil War had Iron Man fighting (with papers rather than fists for a change) against the registration act in Washington D.C. (together with Peter Parker). When a primary school full of kids blow up in Stanford during a run in between reality TV Superheroes New Warriors and the supervillain Nitro, Iron Man changes his mind and decides to team up with Reed Richards, Henry Pym and the U.S. Government to hurry the act along, going far enough as to set an incredibly short time limit for all superpowered beings on US soil to register (and in the process become government employees) or be hunted down and chained up in a superprison in the Negative Zone. Spider-Man unmasking at a press conference is a huge win for the pro registration side, gathering a lot of attention, and several heroes sign up because of it (meanwhile, the villain actually responsible for the Stamford Massacre runs free and ignored by everyone save Wolverine and Namor). Formerly imprisoned villains, some of whom are among the worst sociopaths Marvel could muster up (I'd like to remind everyone that not all sociopaths are bad. Some of them are Sherlock Holmes and Dr. House) are released under the Thunderbolt moniker to hunt down Captain America and his allies (mostly street level heroes and youngsters).
This is a dark story. Even if Marvel made a horror movie involving League of Monsters or the Night Shift, it wouldn't be this dark (Please be something that happens. Please be something that happens). I've seen Deadpool/Punisher team-ups with less bloodshed. Even the Joker at his worst in The Dark Knight didn't kill school full of kids. I mean sure, hospital, but at least he was kind enough to warn them in time to evacuate. The story reads like a dark caricature of the nightmare NRA wants us to believe will happen if restricting gun laws pass in the Senate.
Considering this, and the fact that out of all heroes and villains in the entire Marvel Movieverse, the Winter Soldier and (maybe) Ant-man are the only ones government agencies don't know the identities of anyway, I wouldn't hold my breath for a Civil War movie with the Pro-/Anti-registration conflict. Also, as it turned out in Captain America: the Winter Soldier, the senator who sought out Tony Stark for a battle of wits over the Iron Man technology in Iron Man 2 was an agent of Hydra. Even if the Stanford incident (or something similar) happened, I wouldn't bet on the movie version of Tony backing the government in anything control-related for a while yet.
I think this is a good spot to remind you all that Captain America and Iron Man are the only ones in my synopsis Marvel still holds the licence for to use in movies (well, there's Hank Pym, but he turned out to be a skrull, so...)
I'm not going to just bash the idea of a Civil War movie without giving a couple thought out possibilities for the title. After all, Age of Ultron will be very much unlike the Age of Ultron of the comics. There's no reason we shouldn't expect the same for Civil War. So here's a few alternatives.
There's the literal approach. It's likely we'll be introduced to the Inhumans in the next couple of years. Possibly even before Avengers 3 turns up. Recently the comic event Infinity bled into Inhumanity, where the Inhuman king Black Bolt faced with the likely extinction of his people spread the terrigan mists over the world, turning everyone with an ounce of Inhuman blood in their vains into fullblooded, powered inhumans. That's the kind of ending I could see an Inhuman movie could end up with, making Avengers 3 take place in a world of humans with a superpowered minority of inhumans (who needs mutants anyway?). Inhuman power structure being what it is, I could easily see a struggle between Inhuman royalty and a larger band of rebels, making it an Inhuman civil war where Avengers will have to intervene. For all we know, the source of the terrigan mists could be one of the infinity stones, making it a likely destination for Thanos and the confrontation the movies have been building up to.
In Ultimate Marvel, a parallel comics universe to Marvels main continuity, Peter Parker the teenaged Spider-Man fought for his life, and lost. The reason nobody came to assist him (well, Iceman and Human Torch did, but they ended up passed out in a ditch somewhere), was that the bigger heroes of the Ultimate universe were engaged in battle with each other. Nick Furys underground Ultimate Avengers were up against SHIELDs New Ultimates, both sides certain that the brains behind the other side were selling military secrets and weaponry to terrorists. Neither side wanted to kill the other, just make sure they stayed down so they could bring the imagined culpit in and show the other side that they were in the wrong. It's an easier “Civil War” to make on account of needing less people, and not being reliant on ideologies that might not sit well with everyone. I don't like the idea, but it's a possibility nonetheless, and one far more likely than taking inspiration from the actual Civil War event.
My third option is pretty much just Mind Control. Throw Thanos into the mix with some subtle tricks to turn everyone against each other, then at their most divided swoop in and invade the planet. It's inelegant and hardly worthy of the name (though Avengers: The Infinity Gauntlet has a nice ring to it), but it's the best third option I can come up with (which is probably why I don't work as a screenwriter).