He's dead, Jim.
Joss Whedon, writer/director of both of the Avengers movies, executive producer of SHIELD, and adviser on everything MCU explained his reasoning recently in this interview.
A lot of people come back in The Winter Soldier. It’s a grand Marvel tradition. Bucky was supposed to die. And the Coulson thing was, I think, a little anomalous just because that really came from the television division, which is sort of considered to be its own subsection of the Marvel universe. As far as the fiction of the movies, Coulson is dead.
To Whedon, Coulson isn't alive in the movies, and thus, can't be in them.
I believe this additional information comes from SFX magazine (Buzzfeed, ever the quality news source is not clear here), but Whedon made another similar comment, further explaining why he is not in the sequel.
“As far as I’m concerned, in this movie, Coulson’s dead,” he said. “If you come back in the sequel and say Coulson’s alive, it’s like putting fucking John Gielgud in the sequel to Arthur. It mattered that he’s gone. It’s a different world now. And you have to run with that.”
IGN got a bit more out of Whedon in their interview, where he explains that he's making the movies so that they are completely self-contained for viewers who only watch the movies.
“It’s a weird little yes and no. As far as I’m concerned in the films, yes he’s dead. In terms of the narrative of these guys [The Avengers] his loss was very important. When I created the television show, it was sort of on the understanding that this can work and we can do it with integrity, but these Avengers movies are for people to see the Avengers movies and nothing else. And it would neither make sense nor be useful to say ‘Oh and by the way remember me? I died!’”
With Whedon taking a further step away from the MCU, this could change in the future.