Ive been working on this mockup for a few days now and Im getting really tired of it so I figure I would post it before I abandon making it.
My idea that I have never seen implemented in file management is called pathview or perhaps webview. Maybe its already out there but I have never seen it, I think it would be quite revolutionary and genuinely useful if ever implemented.
Pathview/webview: All files are presented in a single window; the user is able to move around the files like in an RTS game or Google Earth. An excellent example of this implementation would be the game Defcon. The user is able to zoom in and zoom out and follow the mini-map in order to locate files.
Organization: Essentially you could create areas for files, like a map. It could be based on the world, planets or anything else. You can move files around by dragging them to different areas with out actually changing their position in the file system. It simply makes no sense that we have to follow the organization of our operating system in order to locate files. The line paths would still indicate the original location of the files in the file system even if the files are placed in other parts of the map.
File movement (not in the mockup): One problem with pathview could be moving large amounts of files. To speed this up, the user has a special tool. A temporary folder or basket, which allows the user to place files into this area temporally. Then move into another part of the map and move the files into that area by dragging them out of the basket. This is similar to the way that RPG games implement item management.
(Icons used in the mockup are called iVista)