How to realistically manage folders in SP 2013

I have been tasked to roll out SP to various departments within a division.  My initial hope was create 1 doc library for each department and associated content types and meta data.

However, for one department the manager said it was unrealistic to expect his team to load files 1 by 1 and then select/choose the appropriate meta data/content types.  Thus, I have 2 issues:1) A method for the user to load multiple files at once and 2) How to capture content types and meta data.

For #1 this is easily resolved by telling the user to use Windows Explorer or Harmon.ie (An Outlook add-in).  #2 is a little thornier as it seems like for this department I am forced to use folders and depending on what folder receives the file then I can default the content types and meta value.  However, a major selling point of SharePoint is to be able to easily search and manage files.  Can someone give me some advice on how to manage the file/folder structure for this particular department ?

I need to avoid the situation in 6 months where the SP folder structure is so out of hand I was better off having the department not use SP and use the file server LAN.