If you read Iron Man comics, you would know that in the Extremis series Tony removes the Ark Reactor due to modern technology. The reactor's sole purpose was to create an electro magnetic field capable of holding the shrapnel for long periods of time. The suits themselves are equipped with their own Ark Reactors, as seen in the chest plates of every single suit/drone. Instead of an empty hole like it once was.
Now in the comics, Tony Stark does retire as Iron Man and gives his position to Rhodes. The whole shebang that happened, if I remember correctly, is that Iron Man faked his death, and Rhodes flew from the ashes in his custom suit taking the position of Iron Man.
With the switch up they did making Rhodes the Iron Patriot, instead of Norman Osborne, they still made it similar to the comic story line. Tony retires, and Rhodes keeps working.
I imagine that in Thor 2, which will be setting up the main story along with Winter Soldier, when Thor lets Loki out of prison, he will go rogue once again. Somehow landing Tony Stark in prison, like in the comic. Relying on Pepper Potts and Rhodes to help him escape, where he will then create more suits. Seeing the movie went up to 40 something, compared to the 150 or so armors created overall.
The ending showed that he kept Jarvis and Donnie, while he towed them away. Insisting that he will be using them again in his future lab.
So my thoughts are that there will either be an Iron Man 4, or Avengers 2 will be Iron Man based.