First, let's begin with this picture taken from Comic Con this year:
This poster gives the future film titles for the next phase of Marvel films.
Now, spoilers ahead for anyone who hasn't read the comics, or hasn't seen the Avengers 2: Age of Ultron trailer in some way.
In the Age of Ultron trailer, there's a scene where the Avenger's members attempt to lift Thor's hammer. None of them appear to be able to lift it, before an ensuing attack from Ultron occurs. For those of you who have seen it, there's a line spoken by Tony Stark referring to using Thor's finger prints to be able to lift the hammer, which is debunked by Thor in a very joking manner.
This has already set the tone for a major event within the Civil War story line, but I will return to that in a moment.
Looking at future Marvel titles, the title for the third Thor film appears to be Thor: Ragnarok. During the events of Civil War, Thor was away in Asgard, for the battle of Ragnarok. However, this did not prevent Thor from making an appearance during a battle between Stark and Cap forces.
How was Thor at Ragnarok, but also on Earth for the Civil War? Easy.....Mechanical Cloning.(Not so easy) While in the comics it was Reed Richards responsible for the cloning and eventual appearance of the mechanized Thor, movie rights with respective studios may obviously get in the way of that.
Bringing us back to the theory made by Stark concerning copying Thor's finger prints. To clone Thor, who needs the genius of Reed Richards when you have the genius of Tony Stark?
It's my theory that Stark's comments meant something. Something he could possibly just be rolling around in his head, or a possible act of war.
Let's not forget how much of a big deal everyone has been making of Thor's first appearance in other films.
Killian's remark in [Iron Man 3](movie:24391)
Fury's comment in the Avengers
People genuinely see Thor as a threat and someone possessing great power. To control him would mean great power.
Will Ultron be the final straw for Stark? Will enough loved one's finally be hurt or lost that the power of Thor must be utilized for personal use?NO
Anyone who has read Civil War could probably agree that T.I. got his role in Ant Man just in time for a Civil War film
Got the juices pumping yet?
BONUS THEORY: BILL IS COMING!
Many people have spotted what appears to be Beta Ray Bill among the Collector's collection. I will support this, as Beta Ray Bill is a very cosmic character, being very appropriate for the Guardians of the Galaxy setting, as well as being a prominent character making an appearance at Ragnarok during the Civil War.