[Spoiler Ugh.

I shouldn't have watched Ultron tonight. I won't spoil anything in case you haven't see it but Coulson's (in the eyes of Gonzalez and his Real!SHIELD allies) make so much more sense in the finale and ending scenes of the movie.

Obviously the movie doesn't mention Coulson specifically, it connects a lot of dots in the show.

Spoilers (Spoilers) 1. Around the middle of the movie, Fury appears for the first time to the Avengers and gives them a pep talk and discusses with them on how to bring down Ultron. He them announces he's leaving with Maria Hill, and Stark makes a cynical and suspicious remark, believing she was always in Fury's employ the entire time. (Much like how, Coulson is in Fury's inner circle). We don't see him until the final arc of the movie ends with a giant SHIELD Helicarrier helping evacuate Sokovian citizens from their nation/city, which has been lifted far above the clouds by Ultron(who is intending to smash the immense landmass into the Earth, creating an extinction-level event that will wipe off all life). While the episodes themselves aren't out yet, I am heavily biased towards the idea that before and concurrently with the movie, Coulson settled out any internal fighting and was contacted by Fury to pilot one of his (seemingly limitless) Helicarriers, and that he, his SHIELD team, and any defectors from the Real!SHIELD were the ones piloting and defending the Helicarrier from Ultron on their way to Sokovia.

At the very end of the movie, the Hulk goes into hiding, Thor leaves indefinitely, and Stark unsurprisingly quits the Avengers. Captain America and Black Widow remain and begin to train the New Avengers(Scarlet Witch, Falcon, War Machine, and Vision). The beds, housing, food, and money that Gonzalez was accusing Coulson was burning through? The searching for powered people on The Index? It is heavily implied if not flat out stated that all of that was Coulson constructing Steve and Natasha's avengers academy, as well as finding Fury potential gifted recruits for Steve and Natasha's training. Even after watching the movie Theta Protocol is still unclear. There was some expository at the very beginning that basically said The Avengers' raid on List's compound for the Scepter was the last one of many, and that this wasn't The Avengers' first time raiding an enemy compound (for the Scepter) since the end of the first Avengers. The best explanation of Theta Protocol as I understand it is Coulson's command for the Avengers to group up and raid a location or attack a target. Basically Maria Hill is a proxy for Coulson's intel in the movie. Basically, all of this leads me to believe Coulson's going to come out on top at the end of this season, and the hypocrites, myopic rogue SHIELD agents, and bigots like Gonzalez, his allies, and likeminded SHIELD agents will be killed or left in the dust.] (/spoiler)