What a lot of people don't realize is that the Star Wars series that have come out over the past few years don't necessarily aim to bring back the classic actors. Lucasfilm has preferred to do new things with new characters or explore parallel storylines, so it's not like there's any drama between McGregor and the studio - it's just that the projects are going in different directions. The guy's been doing a ton of work in indie films, psychological thrillers, and that kind of stuff that apparently motivates him more at this point in his career.
What's interesting is that when there was that Obi-Wan series a while back, he did come back. Since then things have been quiet on his end, but that doesn't mean he's closed any doors or that he has conflicts with anyone. It's just how the industry works: actors and studios go for what interests them at any given moment, and if the projects don't fit, no big deal. Sometimes it's a timing thing, sometimes it's money, sometimes it's just that someone decided to tell a different story. No drama.