My thoughts is that by the end of the first season team Coulson will be Away from shield and working as the MCU version of the secret Warriors.
I'm not familiar with them, my involvement with the comics ended 20 years ago and never spanned too far away from X-men & Spiderman comics with any regularity.
I am expecting to see the AOS as well as the netflix heroes show up in AOU, and I think were going to see an episodie of AOS next season tie in with GOTG.
That might happen, but AoS will be on break during the release of GotG, unless they do a special 2hour episode in the off season (I don't see that happening, and the fact that Feige said that GotG takes place on the other side of the Galaxy, which means it's ties to earth, and SHIELD should probably be almost non-existent, unless something happens at the end of the movie that would bring them here) which I really don't see happening, as it would also interrupt with whatever happens between s1 finale and s2 premiere.
Its hard to do a crossing of streams when a TV apperance usually counts towards one of an Actor's contractual apperance. (Trust me Marvel is kicking themselves that they wated RDJ on the Incredible Hulk). Were probably going to start to see more side charcters introduced into Agents of Shield.
Yeah... see the story about New Avengers Phase 4 up above.
It's also a reason I've asked before it it's possible that Marvel starts new contracts with separate Movie and TV appearances in the contracts, now that they also have Agents of SHIELD, which is sorely missing appearances from big characters such as Stark, Banner, Rogers, Thor, Widow, Fury, Hawkeye, etc etc.
It seems at this point they are negotiating TV appearances as they arise and some of the more major characters command too much of a paycheck per appearance, so it would be nice to work some TV appearances into the contract separately.
I'm sure the Defenders wouldn't be much of an issue as they are already on seasonal TV contracts, I'm sure they would be more than happy to cross-pollinate other TV series to get a shot at becoming popular enough to join the movies, and/or just keep their own series going.
I know AoS is slowing addressing problems with guest appearances, because they wanted to initially "stand on their own", but we are past that now, it's time to bring out some big guns and infuse the TV show with some of the charm and grandeur of the movies (or atleast the style of the One-Shots). I know Lady Sif is coming, and rapid expansion is about to take place
Lorelei - sister of The Enchantress, DeathLok, Graviton, Blizzard, whoever Skye and The Clairvoyant are, but we need an appearance from Steve Rogers (Black Widow & Hawkeye) assisting in the field, Stark and/or Banner assisting in the Lab and Thor consulting on "magic" or Loki causing some mischief.
and speaking of Loki, and how Loki secretly wants to be Thor...
He actually tried to be.
http://io9.com/behold-tom-hiddlestons-shirtless-audition-for-the-role-1511013061 (of Thor)
(From the Thor 2 DVD due out Feb. 25th)