I'm a great proponent to a folder structure. But personally, I wouldn't care how Calibre saves it on disk. If I do find one fault, it is that you can't have a folder-like structure within the application itself (select Author: show books of authoor, then select series: sow books of that series by that author). This goes beyond search or ordering. It is more like filtering.
Once I found out I could save my books in any folder structure I like, using the save templates, I started using Calibre. No matter the way it saves it on disk.