SharePoint robust features can be offset of bring the mess from a file share/shared drive and just simply bringing a new environment without cleansing the documents first.
Windows Server 2012 R2 has a great feature to help tackle the information explosion prior to migrating all your documents into SharePoint called Data Deduplication.
Data deduplication will allow your organization to help cut down on the number of “like” versions that can be scattered across numerous folders.
As a result, you get down the “single versions” of the truth with your primary documents. Then you can take full advantage of search, records management, etc. within SharePoint to help your organization save money with regard to storage and time to search for vital information.
Here is the article on how you can use data deduplication in Windows 2012 R2.