Without indulging in any major spoilers, Captain America: Civil War would seem to make re-assembling The Avengers for their next scheduled group-outing in the Avengers: Infinity War films (or whatever they will eventually be called) a fairly difficult prospect. So things are likely to get worse before they get any better, and the various films leading up to the two-part event may wind up detailing how certain aspects of the MCU recover from the fallout of Civil War.
But according to the filmmakers behind the upcoming blockbusters, keeping the roster officially separated between films won't be part of the equation.
Though the idea of a "completely new" Avengers team appearing in the third team-up outing has long circulated and the presence of two different installments seemed to make a divided team more likely (especially being preceded by Civil War); speaking to IGN screenwriters Christopher Markus and Stephen McFeely explained that a direct divide wasn't in the cards. McFeely had this to say:
"When we're outlining it, we had those conversations. I mean, in the same way that in Civil War not everyone has the same amount of scenes or lines, I think you can assume that with so many characters we'll have to be as rigorous: These people will have larger stories, while these other people will have smaller stories. Hopefully they can flip - I know a few off the top of my head that have a small part here and a bigger part there."
In other words, while a multitude of characters will be present in the narrative, some will have arcs that that figure predominantly in one sequel or the other -- which would make a certain degree of sense, given that we're talking about characters with widely varied abilities, and also about a situation where (as of now) some prominent figures might need more convincing than others. Markus followed up his co-writer's comments by saying:
"Characters in the foreground in one film might be in the background of the next. There will be, you know, moments where every last damn person who's still alive will be in the same room, and they're just a nightmare to write because... Marvel being very good about hiring very good actors you have, like... the fifteenth person there has two Oscars."
The premise (and full character lineup) for the two films is still a closely guarded secret, other than that outer-space villain Thanos and the Infinity Stones are expected to drive the main plot. One thing being left unsaid in the speculation over the size/makeup of the Avengers team is that not every Marvel hero in attendance necessarily needs to be an Avenger. Along with separate teams like Guardians of the Galaxy potentially appearing, it's plausible that other potential players like Doctor Strange, Captain Marvel, Spider-Man and The Black Panther may not necessarly align with the "main" team.
Captain America: Civil War is in theaters now. Doctor Strange opens November 4, 2016;Guardians of the Galaxy Vol. 2 – May 5, 2017; Spider-Man: Homecoming – July 7, 2017;Thor: Ragnarok – November 3, 2017; Black Panther – February 16, 2018; Avengers: Infinity War Part 1 – May 4, 2018;Ant-Man and the Wasp – July 6, 2018; Captain Marvel – March 8, 2019; Avengers: Infinity War Part 2– May 3, 2019; and as-yet untitled Marvel movies on July 12, 2019, and on May 1, July 10, and November 6 in 2020.