I am adding this suggestion to the other similar requests.
I understand the project folder with multiple schematic pages linking to a single pcb.
What I thing might be an easy additon to suppor the needs of multi pcb projects is a project colletion folder. This folder could hold each of the project folders as they are now and make it much easier to manage projects in the UI.
Multiple levels would be great but even one would be good.
Brand new interactions and interfaces. 
Easy to use and quick to get started. 
