Calibre is open source and if you don't like how it handles something, you're more than welcome to make changes or pay a programmer to make changes for you. Calibre is a book management system and there are reasons that it wants to manage its database a specific way.
If you don't like how Calibre works, feel free to use your own directory structure and use Calibre only to convert formats. You'll need a few extra steps, but then you can manage your books your own way.
Also rememember that Calibre is free and no one is forcing you to use it :-)
Last edited by animedude01; 07-08-2013 at 12:19 AM.
Reason: Grammer and typos