I found the series as a whole confusing and messy. There's a theme, but, what exactly it is, I don't know. The story is told backwards -- by that I mean the first book has the conclusion to the series while the subsequent books build up to it. But, there is the ultra befuddling current timeline that picks up with the second book with flashbacks to the "future".
As the Kinks sang in Lola, "it's a mixed up muddled up world".
I was incredibly disappointed by the end of Acceptance -- I had NO idea what I just read nor how it properly fit in, nor, did I feel there was ever any sort of resolution. It's a terribly disconcerting and jolting style of story-telling and not one that lends itself well to, well, anything.
I'd highly encourage Mr. VanderMeer to consider taking a basic course in narrative and flow. Based on this train-wreck of a trilogy, I sincerely doubt I'll read anything further by him.