Now my memory of the book is from a while ago and I don't know if everything is accurate, but here's a brain dump of all that I've got.
I read it 6-ish years ago, it wasn't very old though I can't remember the computer technology referenced in the book that would give its age away.
Main character is male. There is a female character who may be his daughter. The main character is human on an alien world with a variety of species. He may have been a representative of humanity to this other world. He stayed on this world for a time, came back for a couple years, then returned because he couldn't stay away.
There is a kingdom style leadership on this world. The overseers are intelligent and vastly technologically superior. The "crazy" overseers are actually children of that species. There is something in the sky (an aether?) that destroys most things but the overseers have ships that can travel through them. The ships work by you thinking where you want to go.
The female main character is made blind and sent to live with psychic animals. The psychic animals group together to enhance their psychic power and rebel against the overseers. she records her experiences in a book by pin pricking it. She has the option to get her sight back with overseer technology, but she provides them with the ability to see everything that she is doing then.
The male character is about to blow-up the overseers main fortress when something happens, he was going to use an antimatter bomb. He ends up getting his memory wiped by the overseers, I think a female one.
I've scoured NPR's Top 100 Sci-Fi books list and it's isn't on there. Neither is it on http://bestsciencefictionbooks.com/top-25-best-science-fiction-books.php.
Thank you for any help you can provide!