I tend to have quite a few situations where it is appropriate to keep a single file (or folder) within multiple folders in a classic 'many to many' relationship.
Under the old Chrome/Win7 interface that is pretty easy to manage. You can see what is going on from the checkboxes in the 'Move' window. So take a file/folder that is already in two folders and you can add it to a third and fourth with a real expectation you can succeed in the task.
With the new interface there are a few document specific features to manage, say a Google Spreadsheet from its editor window. For a pdf, jpg or folder, only the new 'move' window stripped of checkboxes is provided. I have tried all sorts and simply have never succeeded in achieving the task set out above of taking a document already in two folders and adding it to a further two.
It may well just be that this functionality is lagging but I really wouldn't like to see the ability to put files/folders into multiple folders deprecated because to me it is Google Drive's little publicised killer feature.
In the older interface you can make multiple selections of files which have various combinations of folders they are associated with in order to say remove them from the current folder and add them to another one without disruption any other folders they are variously contained in. Even the multiple selection is now prevented.