So I was thinking, since Marvel is pulling elements from all different comic books....... it might be reasonable to presume that maybe (and here is my crazy theory)....... Well first we need to go over some things.......
First of all The Tesseract/Space Stone was in Captain America: The First Avenger, and The Avengers and it is currently in Asgard (Loki may have access to it).
Secondly, The Aether/Reality Stone from Thor: The Dark World is on Knowhere in the Collector's Museum.
Thirdly, The Power Stone from Guardians of the Galaxy is on Xandar in the possesion of the Nova Corps.
(Some say that Loki's Scepter contains the Mind Stone, but I do not think it is)
So what I think will happen over the course of the series is.....
Since Doctor Strange is all mystical and Sorcerer Supreme, etc., I think either the TRUE Mind Stone or Time Stone will be in this movie.
And with Adam Warlock's cocoon seen in Thor: The Dark World and Guardians, it is likely to presume that Adam Warlock and the Soul Gem will appear in Guardians of the Galaxy 2.
And then, I believe through the beginning of Avengers: Infinity War Part 1 will involve the final stone being collected, along with the other 5 (Unless the Scepter is the Mind Stone)...... and here is where my theory gets crazy. In Part 1 The Avengers, Guardians, etc. deal with Thanos and defeat him..... and different people protect different stones (like in the comics). But the post-credit scene shows Loki hearing about a certain powerful, GOLD object, and then we have Captain Marvel and Inhumans...... and Infinity War Part 2 comes.....and in it Loki has aquired the secret EGO stone, Thanos swoops in, reclaims the stones and reunites it with tho other 6, rebirthing Nemesis, and so The Avengers (+ Guardians, Inhumans, etc.) must stop her. OR something like what happened to the Silver Surfer (when he became Dark Surfer in Super Hero Squad [because the Infinity Sword was the Ego Gem]) happens to Thanos. Either way, it would be an amazing way to end Phase 3 and would be a very climatic story!!!