I'm also a really big fan of the file tree idea for blueprints, it seems so much more organizable and expandable than any item/grid based blueprints system. With the inclusion of item icons in in-game text and sharing settings for blueprints the system would be far more robust than the current. It would also be a lot more unobtrusive in the UI and be a lot smoother to use than item based blueprints.
As for physical transfer of blueprints, an idea would be that you can create a physical item that has the contents of a blueprint or folder, then that can be stored in a chest or inventory. To be placed in a user's library, they can either use the item like a consumable and it would be placed in the root directory of the blueprint library, or it can be put on the cursor and placed in a specific location in the library by clicking. The physical item will be consumed and removed from its containing inventory. In the case of an existing blueprint, there should be a prompt to replace, skip, or rename the transferring blueprint. In the case of an existing folder, merge, skip, or rename should be the options. Any skipped files/folders should remain in the physical item and not be consumed.
The default sorting method should be lexicographical with folders and subfolders, but pure lexicographical, date last modified, date used, and type/subtype should be implemented. The type field is an optional field in the blueprint's metadata that can broadly define the use of a blueprint eg. "smelting/iron", "production/green circuit", "logistics/train/loader", etc. When sorted by type they should be displayed in trees like the default sorting.
The last thing, which is not needed, but would be helpful, is a way to organize blueprints via chat commands. Like /bdel ./prodution/greens/testbuild to delete a blueprint/folder at that path. /brn [path](rename), /bcp [path](copy), /bstr [path](outputs/links blueprint/folder string in chat), /bsav [dir](saves last blueprint in chat to [path]), /bexp [path]|[local storage dir] (exports string to text document at [local storage dir], defaults to %APPDATA%/Factorio/Blueprints), and /bimp [local storage dir]|[path] (previous, but for imports) are also command suggestions.
Any sort of feedback on my suggestions would be appreciated and I will update this post as necessary.