If you aren't up to date on you MCU movies, be warned that spoilers will follow. If you've seen everything up to The Winter Soldier and AoS, then read on. There is a rumoured spoiler included as well, and I don't know how to format for roll over exposure yet, so forgive the space block.
The key points for my thoughts on this possible direction for future movies begin with the dissolution of SHIELD, and Agent Coulson now taking the directorship. We also know that Stark was quite proud of his "Privatization of World Peace" in Iron Man 2, making this move all the more logical. With no more Iron Man movies apparently in the pipeline, I think this is a great way to keep the character relevant in the MCU without centering movies around him and having RDJ work for an entire movie. The end of Winter Soldier also saw Maria Hill applying for a position with Stark Tech. With Tony now funding the Avengers, I think it would be quite within his arc to have him take the wheel from Coulson and run SHIELD.
There have been rumors that POTENTIAL SPOILER
Cap will found his own team by the end of Age of Ultron, which could leave Iron Man to use his new Extremis powers to run the World's largest defense system.
This is where my speculation begins. If Cap does find Bucky and try to bring him back to the real world, he could be faced with huge backlash since all of SHIELD's files have been exposed, likely including some bad things Winter Soldier got up to, or some level of destruction from a Hulk rampage. Steve could see that having a secret identity is important for heroes to be able to separate their private lives from the constant danger that their lifestyle brings. Any number of things could happen to force public opinion to have SHIELD register heroes and detain vigilantes. I know that directors have mentioned in the past that there are some notable key characters from Civil War that Marvel doesn't have liscence to, but I still think they could make this work quite well after the introduction of the Defenders, Ant-Man, and possibly even the twins in Age of Ultron. Heroes like these along with Winter Soldier that aren't as palatable as such for the public could end up being chased down by Tony's SHIELD.
I'm not sure how they could fit this into their current slate of movies, but I'm still hoping that if Ant-Man can do anything like what Guardians has done in the box office we could see more movies being added to that slate. Another thing I would like to see is the now "Deep silence" Fury develop some Secret Avengers. I think he is already on his way to doing this as we saw him ask Falcon to join him in Europe as he could use his skill set. I'm making an assumption here that he takes Hawkeye with him, and this is how Barton ends up freeing the twins at the start of Age of Ultron.
A lot of speculation, sprinkled with some hope on this article, but let me know what you think. I haven't thought this out very deeply either, so if you have ideas to add I'd love to hear them in the comments.
Make mine Marvel!