Well the fundamental flaw is that the view presented to the user is rooted in the representation the filesystem implementor chose, the user should effortlessly

Well the fundamental flaw is that the view presented to the user is rooted in the representation the filesystem implementor chose, the user should effortlessly be able to switch between different views and add additional ones, Apples' "All My Files" together with the ability to filter and save those filters is brilliant and very much in the right direction, although it should support some form of join operation. One idea would be, that in addition it should be possible to execute computations on the current view of the filesystem and the possible computational primitives are selected by the "type" of the files (essentially find a way to lift a typed version of the unix shell with pipes to the GUI level). Another idea would be to emphasise versioning and time based information more. For example with the current storage capability it makes little sense for the default save operation when working on a document to be "destructively replace the old one". Obviously as a programming one is aware of that and uses version control systems, but so far I had multiple occasions when working on a collaborative project not involving code, where the versioning was done by appending suffixes to folder names.