So with tonights release of Variety's article of Robert Downey Jr being in Captain America 3, it looks like we are getting a Civil War storyline into the MCU. But to be honest, I think Marvel was going there already before this announcement. As seen in The Winter Soldier, there was already the distrust of SHIELD(through the workings of Hydra) to the American public. Now with Tony Stark inventing Ultron, as a help to the Avengers, the American public and the world will be even more distrusting when Ultron goes on a rampage. This sets up the government to set up the Superhero Registration Act. I believe the ending of Age of Ultron will set in motion the beginnings of Civil War which will be seen in Captain America 3 and most likely Avengers 3.
Now some of you may be wondering, will what about the Infinity Stones/Gems & Thanos. How does this factor into all of this. Well, besides those two movies that I stated above in Captain America 3, and Avengers 3 the rest of Phase 3 will be dealing with some part of the Infinity Stones/Gems. I believe Guardians of the Galaxy 2 will end with Thanos on his way to Earth. This then leads to the end of Avengers 3, where we have an epic battle between Iron Man and Captain America and just as it seems they are about to both deliver the fatal blow to each other, Thanos arrives on Earth and scene cuts to black.
This lets Marvel make Avengers 3 and Avengers 4 back to back. Now Avengers 4 will not be a adaption of Infinity Gauntlet but of Secret Wars. Thanos uses the stones to send all of the heroes and villains that we have met to Battleworld. So in essence Thanos becomes the Beyonder of the MCU. This can lead to two separate ideas, you either have all of the MCU characters there or Marvel, FOX and Sony strike a deal so that the X-Men, Spiderman and Avengers can all be in one movie. In having the X-Men and Spidey be there, you can say that Thanos opened up different dimensions and universes. So at the end of the day, the X-Men universe and Spidey one can be used but it wouldn't affect the continuity of those movies. I say an example would be at the end of the movie, the universes all get restored and everyone memory of the event could be erased, so that again the FOX and Sony properties can go on without any problems.
If they go with just the MCU characters, you could have some of them sent there while others are left on Earth and have to fight Thanos' army. In the end, the villians and heroes team-up and defeat Thanos, return to Earth and defeat the rest of his army. This is where I would put the death of Steve Rogers, so that1) to give a more emotional impact to the story and to Tony Stark and 2) Bucky could take the mantle in future movies. As a side not, I can see Marvel killing off Rogers in Captain America 3 and have Avengers 3 with Bucky.
So this is my ideas for the future of the MCU, what do you all think, hit the comment section!