The article I'm citing doesn't bring this up, and maybe it's better not to ask, but I do have to wonder whether one of the factors still isn't transphobia here? Then again, maybe the movie is just too challenging to get the kind of mass-think following that it takes to get an Oscar nomination?
Anyway, this article, from someone who clearly admires the movie, focuses on some of the aspects one would have thought would have almost guaranteed a nomination. I admit I'm a little disheartened that it faced such a shut-out on the nominations front.
Why No Oscar Love for Cloud Atlas? (http://www.denofgeek.com/movies/24048/why-no-oscar-love-for-cloud-atlas)
A web search will find a fair number of similar articles from various perspectives.
I can't say I was entirely surprised, given how the movie was treated with mild dystain from many self-satisfied critics, who seem to object to anything that contains "too many" ideas.
I'm not terribly surprised, but it is a little saddening.
Personally I don't think transphobia played a role in the reviews this movie received. People simply don't want to be challenged by cinema, which is why Inception (a movie that was sophomoric at best) did so much better.
I do think he Coud Atlas will become an essential part of movie history, particularly in schools, for both it's successes and failures as a movie.