Originally Posted by sensoria
(3) Organization can be iffy. I use Shelves (easy with Calibre and the metadata plugboard) but each book/fic can only be in one shelf -- there's no way to add it to multiple shelves (as far as I know). So deciding how to set up your Shelves takes some thought. If you only read one fandom, for example, you could set up shelves by genre & pairing; or if you only read one pairing, by genre & rating. Etc. Whatever works best for your collection.
Not sure if that is a limitation of the Calibre plug-in, but it is possible to add a book to multiple shelves on the device itself. I tried it with a regular e-pub if that makes any difference.