Flat Document Libraries vs Folders

Jahongir...always use metadata where possible and NOT folders.  The only reason I use a folder is for specific use cases where I need that level of security.  Some strategies that I use are:

1. People have been working with folders as a way to organize their information forever.  They can't find anything and duplicates are everywhere.  
2. Setup a working example of how using metadata is more advantageous.  I use an invoice document library.  It demonstrates the possibilities of having multiple search scenarios.
3. Make sure you setup your information architecture with content types so you can use Search and Refiners to further find information.
4. When trying to define metadata, use the folder structure they have and file naming convention as a starting place.  Users will understand this because they created it, plus it demonstrates how to better find what they are looking for in ways they have never had in the past.

As I lead users requirements sessions always consider security and how they will find the information.  This will drive the metadata discussion.  You'll need to do a lot of hand holding initially until users understand it, but once they do they won't turn back.

Hopefully this helps.

Steve