While I can somewhat understand the deep techie need to manage down to the file level, I never quite understood why people practically require it as a feature on MP3 players. The empeg pretty much showed very good reasons for using a database method for music, I can't imagine having a drag and drop MP3 player with gigs of music.
A good compromise would be to let the device accept files via drag and drop, but then internally have the software on the device add them to the database. That way you can get away from poor syncing software, but still get the benefits of having a database.