'Agents Of S.H.I.E.L.D' has hinted around that Coulson isn't what he seems. He feels different. He's having nightmares. He's not being himself. Obviously something is up and I think I know what.
After the battle of New York, Coulson died and Nick Fury gave an order to bring him back. Using a Life Model Decoy, Shield brought back Agent Coulson. To help him accept life they kept him from the knowledge of what he truly is.
Through out the series (possibly just the first 2 season) Coulson will slowly start to realize what he is. He already questions himself and his suspicions will continue to grow in future episodes. Once he finds out what he truly is I imagine 1 of 2 things will happen.
Option #1
Coulson discovers his true nature. He accepts it and joins the Avengers as the android "Vision".
This would make sense for a few reasons. Coulson was always a well received character. If Marvel chose to turn him into Vision they would be able to insert him back into the movies and not have The Avengers question why Coulson is suddenly alive. Also with Scarlet Witch appears in Avengers: AOU Vision could be a possibility.
Then there's.....
Option #2
This is my personal favorite. Coulson will discover his true nature and be disgusted by it. He will begin to hate Shield for turning him into a monster and playing "god". He will eventually turn against Shield and become...ULTRON!
This would make sense for a couple of reasons as well. Again, Marvel would be able to insert Coulson back into the movies in "Age Of Ultron". Also, taking a character The Avengers cared for and turning him against them would add an extra layer of drama to the mix. The heroes could be hesitant to fight Ultron since he was basically one of their allies.
There you have it. My theories on what will happen with Agent Coulson and how it could affect the MCU in the future. Let me know what you think will happen with Coulson.