Well I think AoU and Cap 3 are supposed to setup Civil War, all the movies and TV shows after that leading up to A3 or A4 are introducing lots of new characters.
I don't know the storyline, but there should be plenty of heroes to divide before Thanos shows up to crush them all into reuniting again for the greater good.
edit: BadassDigest claims to have been scooped on this story, and offers more insight into everything surrounding it.
http://badassdigest.com/2014/10/13/robert-downey-jr-bringing-civil-war-to-captain-america-3/I've been sitting on this for a couple of weeks now, waiting to get an ok from my sources to run it... and I got scooped. Well played, Variety.
Well, here's the story: Robert Downey Jr hasn't been negotiating with Marvel for Iron Man 4 - he's been negotiating for Captain America 3. Yes, Iron Man will be co-starring in Cap 3, which is either going to be called Civil War or Fallen Son - I've heard both names getting tossed around.
And this isn't some small bit. This isn't a cameo. Downey will be shooting 30 or 40 days on the film. He's basically co-starring. When Marvel heard that DC moved Batman v Superman off their Cap 3 date they wondered if they had heard the story and knew that Batman versus Superman wasn't going to match up to Captain America versus Iron Man.
I'm not clear on how the Civil War story will play out, since the Marvel Cinematic Universe doesn't have secret IDs to reveal, but I can tell you this: the fallout of Avengers: Age of Ultron is going to be huge in this movie. There is a lot of destruction in that film. It makes an impact.
More than that, Marvel is looking at Cap 3 as Avengers 2.5. It's going to be another ensemble picture, and it could feature Cap's new team from the end of Age of Ultron. Last I heard (and they haven't shot this scene yet, so it could change) that team is Falcon, War Machine, Quicksilver, Scarlet Witch and Black Widow, as well as probably The Vision (although I have been told Black Widow will not be much of a presence in Cap 3). And once again the events of a Captain America movie will reshape the Marvel Cinematic Universe.
Remember when I told you Cap wouldn't be in Avengers 3? This is why. At the end of Cap 3 the Marvel Cinematic Universe will be in a tough, dark place, with the heroes scattered and defeated. That will continue through Avengers 3, and it will leave the world open to the threat of Thanos in either Avengers 4 or the big universe-wide team-up movie, whichever comes first.
How closely will Captain America 3 tie in with Avengers 3? I've been told that the Russo Brothers are in talks to direct Avengers 3 and possibly 4. Sources tell me that they're the favorites of Marvel right now and that they are the guys Kevin Feige want to pick up the mantle from Joss Whedon.
tl;dr version:
-RDJ had been negotiating for Cap 3 not IM4
-Cap 3 will be called either Civil War or Fallen Son
-Ironman will NOT be a cameo, but will practically co-star, like BW in Cap2
-Marvel wondered if DC moved BvS because they heard Cap 3 was Cap vs IM....
-Huge Fallout from AoU leads into Cap 3 which is basically Avengers 2.5
-Cap's speculative Team will be (Falcon, War Machine, Quicksilver, Scarlet Witch and Black Widow, as well as probably The Vision)
-Cap won't be in A3 and Thanos won't happen till A4
-The Russo Bros. are in talks to direct A3 & A4, due to how much Cap 3 ties into those 2 movies.
-*Speculation as to how Civil War will playout*:
at the end of Age of Ultron Tony Stark retires from The Avengers and possibly even from being Iron Man. He feels very responsible for what happened in that film, as the Ultron project was his brainchild. Here's my guess for Cap 3: with that in mind, and aware of the destruction his out of control robot caused, Tony thinks that the Age of Miracles is too unregulated. With the fall of SHIELD there's simply no one keeping tabs on everybody. That scene of Black Widow in front of the Congressional committee in The WInter Soldier was a late addition, and it speaks to this - these super beings are answering to no one. And Tony decides that's wrong. Which brings him into direct conflict with Captain America, who is still leading a team of Avengers. I don't think this will follow the exact outline of the comic book story, but simply take the concept and the beloved Marvel idea of heroes battling.
-Not sure if Cap "dies" or just hangs up the Shield (allowing Evans to take time to do his directorial stuff), but he will be back for A4
-**
Spider-man is coming to the MCU - ink has dried on that deal