TWS wasn't a straight adaptation of that storyline, though. It was a synthesis of two.
I'm not saying TWS was a direct adaptation, but that the moral dilemma that leads to Civil War is introduced.
X3 experimented with the idea of controlling the mutant population, and it didn't translate well onto film (though that may have been Brett Ratner's fault).
The same can be said for Captain America, Hulk, and Thor. Let's be honest, no exceptionally huge Marvel ideas played out well before Marvel took the reigns.
The problem with a CW storyline is that it was applied to the entire Marvel universe. The MCU has fewer super characters than the comics, so any dispute is going to be localised in the film when it was worldwide in the comics.
The fact that CW is in a solo film makes me wonder how it will play out. What makes it a CA film and not just Avengers 2.5?
I have this vision of Stark being appointed director of SHIELD and implementing policies that Rogers disagrees with. It might just be a continuation of TWS, where it is just SHIELD vs SHIELD more than heroes vs heroes on a big scale. Honestly, the aftermath and events of TWS should have had more Avengers jumping in.
That's why the Avengers falling out over the defence of Asgard would work - it means leaving the earth vulnerable, creating a dispute that affects everyone whilst retaining a lot of the themes from the comics. And there is a precedent - a synthesis of "Civil War" and "Siege". It could tie in with the idea you floated of Ultron being cast off into space and encountering the Kree, who could then attack Asgard.
For Siege to be part of the story woud require some major events with Asgard in Age of Ultron. Part of me wonders if it will turn out that Thor in AoU is not really Thor, or if something happens to Thor and Stark creates a clone (Ragnorak) to defeat Ultron.
I could see a scenario similar to yours where Thor must return to Asgard before AoU is concluded, Stark creates a Thor clone, and that clone returns to Asgard, believing itself to be Thor. Only it finds out it isn't and becomes Ragnorak. I'm not sure how that affects CW though.
Depending on how the contracts play out Hemsworth might not have room to be in Civil War. The Thor clone may not play a part, which fits the CA solo title.
OK, new thought process: What if Stark leads SHIELD. In Civil War he is just a side character implementing some form of registration act. SHIELD is divided and the movie just follows Cap's efforts with his few buddies that we've met by this point. Depending on how AOS plays out there could be room for bit characters (as far as the movies are concerned) to show up with Coulson. If you bring Black Widow, Hawkeye, Agent May (I could totally see her disagreeing with someone violently), Mockingbird, Agent 13, and so forth into the mix you get a universe-wide cast of heroes that aren't main solo acts.
