Before anything, I purposedly copy-pasted that very question from the Calibre FAQ. Perhaps this is a lone cry from a crazy guy in the middle of the forest but I think it's an important one.
"Why doesn’t calibre let me store books in my own directory structure?"
While in the FAQ is stated that the Calibre "search/tagging based interface is superior to folders" I dare to disagree. In reality I think it's a huge misconception!
This argument may hold some water for normal books (sci-fi, etc.) which you just read once. But it fails horribly, when (like me) you have a library of 20k books on diverse subjects, mostly scientific, you NEED a folder structure like in a normal library! Because :
#1 you rarely look for an author, you look for Science ->Chemistry->inorganic chemistry-> intermetallic phases, not for "J. H. Westbrook" who I don't know and I don't really don't want to know.
#2 When you use reference books... you read them more than once!
#3 It becomes really helpful to have a structure when most of your metadata is wrong or missing.
#4 For sake of OCD people and for the eventuality that you want to give part of your library to someone... it is good to keep libraries separated from each other! I don't want to literally hunt for every author for 30 books on "catalysis" if I want to give it to a colleague!
#5 I don't think it's difficult or impossible to implement. Calibre does the same as iTunes but iTunes can keep the folder structure.
Ok, perhaps I'm overreacting a little, perhaps I'm just absolutely horrified at the prospect of my Library being thrown in a heap after I carefully organized it... but I think this option would make a lot of people very, very happy.
Unless there is some consensus that Flash is evil and kills babies if it runs in computers... oops... sorry, wrong prejudice! But that's how I regard how this option is being handled!
GJMS