I think all the ways to accomplish this are a little un-intuitive for some users. Many, I think, are looking for a way to "open" a file or "add" a book through a menu or other method from within the app itself. Can't say as I blame them, really... it would end some confusion.
But then again, supporting non-Amazon ebooks and actually
encouraging people to read non-Amazon ebooks (not to mention making it intuitive to do so) are two very different things.