even if you perform initial import correctly, iBooks has a lot of issues:
- on Mavericks it's not possible anymore to use calibre to send books to iTunes. Only possible way is to save epubs and manually import them all
- position sync works...strange. Sometimes it works and sometimes it doesn't. Only way to have at least semi-reliable sync is to use manually created bookmarks. -

- highlights data couldn't be exported by regular user (i.e. without messing with iBooks's sqlite db)
Only thing that iBooks (since Mavericks was created) have and Marvin doesn't is OS X version.