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 (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.
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I guess the first step is not to use SharePoint as a replacement for a file system, SharePoint is a collaboration platform and not a document grave. Sure, you can use the search to find topics and content, but the first step in my mind is to teach the people how to use SharePoint.
Saying this doesn't mean not to store files on the SharePoint, it means mainly, that the users are lazy and continue working like they were used before. And if you push tem to add a lot of additional metadata, you will run into a storm of protest.

A lot of document can just be replaced by SharePoint functionality. So instead of putting everything into a Office document and throw it onto the SharePoint, it is more effective (even for the users) to use some of the list / library options, task list etc. to share their information. Document content can only be found by the search while other SharePoint items directly show the content.
I see very often SharePoint sites with hundreds of documents, which never ever will be read again as the users are just too lazy to open 10 documents to find the right information. Even the search will result into more and more hits over the time.

So the first step is to decide, which information is better stored in other SharePoint webparts to avoid the creation of some documents. Especially I like PowerPoint slides on SharePoint, the most useless format at all.
Second I would analyse, which kind of documents are needed on SharePoint. You will recognize, that you have different scopes of documents, some are department related, other project related, the next are global. Also permissions may play a role for a structure. And this may also result into different type of document libraries, some with versioning, others without, and diferen metadata for different kind of documents.

Example: For a specification, technical description etc. it make sense to add several metadata to specify them. Other documents doesn't need metadata and it is nearly impossible to find a common metadata set for all kind of documents. Even metadata can change from department to department.

You will also recognize, that there are different topics within a single department what make it necessary even to create subsites within a single department. Then the point is how to make it possible again to accumulate important data to the department umbrella site.

A often used arrangement is - even to keep it under control from the administrative side - , to build a kind of hierarchy. You can not administrate a SharePoint down to the lowest level, so you have to delegate responsibility to the department itself, so that they may decide themselves what kind of needs they have. Limiting the options at the beginning will result into demands from the departments to the administration what gives you a hint, what they want to have. Then you can decide in which way you make it available. If you let it flow from the beginning, you will find your file system in SharePoint and this is difficult to bring back into a structure.

There is no general recommendation, as every company works different and has its own culture. This you have to reflect in SharePoint to get the acceptance, and on the other hand you have to teach slowly the people to change there behavior away from a simple files system into the direction of collaboration.

Just some thought out of my experience as a start point for discussion.

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upobDaPlayaAuthor Commented:
Appreciate the depth of the response.
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