My current solution is calibre sync. And using justRead.app to read books from the calibre sync folder on my iPhone. This is a bit clunky, but the calibre sync folder is just a mirror of the calibre books, not a separate library to be managed.
I look forward to seeing what you come up with.
I do know that I'm a bit of an outlier when it comes to ebooks. But then, so are many on MobileRead.