So the first Avengers film struggled to use all 6 Avengers. Anyone writing a script for TV or film will tell you that writing a fight scene or story with more than 5 main characters is nearly impossible. This showed in Avengers where Hawkeye spend 85% of the movie as a villain with hardly any dialogue.
Phase Two's Marvel Line-up stars the Captain America, Thor, Iron Man, the Guardians of the Galaxy, Black Widow (Cap 2), and Falcon (Cap 2). With this many characters, will there be any room for Hawkeye? Even if the Guardians don't show up but we get only Thanos from that film, then the roster would still be at six (with Hulk, of course). I'm not complaining because movies have less time to tell a story than the comics do and I like Falcon. But I do think that with no news on Hawkeye, he may not show up in the next film or may have a very minor cameo.
I don't think S.H.I.E.L.D. will show up either since the Avengers became an independent team at the end of the Avengers. I may miss Nick Fury.