The way I thought about it is more or less like there being a ‘create folder’ option when looking at your shelves, and then being able to drag-and-drop shelves into said folders. So the ‘add to shelf’-feature when looking at a game would be unchanged. I guess personally I’m a sucker for hyper-organization, but I do understand there could be issues with implementation.
The and/or shelf filtering options really are gold though. On another note, how about ‘franchise’ filtering when looking at shelves? 