Yes, this can be done using Favorite already but there is no way to set it so that the documents automatically appear in Favorites as unclassified.
To me, this request does not go far enough: I would like to be able to tie a highlight palette to a visual filter to a resource that defined the need or contain the data used to build the filter Similarly notes & clippings (which I can tag), passage lists etc. may also be tied back to a particular resource. Think of it as wanting some metadata on documents.
With that in mind, I'm not sure that a folder structure is the way to go. It may be that documents should be handled in an analogous way to the library to allow the reuse of code and users have to learn only one UI
For those convinced that they want a folder structure one possibility would be to have a Favorites "bin" into which new documents (or resources) of a particular types can be sent to by default. They remain in the unclassified bin until the user moves or deletes them.
