It took me forever to learn how to use Calibre, and set up my books to my liking. Why worry about the file structure. I understand why it's set up the way it is.
You can access your books from the application, filter the view, etc...and when you find what you like you just tell calibre where to put it on your device. There is no need to access the file structure where the books are stored.
I just don't see this new program catching up to Calibre anytime soon. Even if it did, Calibre works just fine for me. If it's not broke, it doesn't need fixing
Wundrbee