It would be great to have the ability to import files and have the source directory structure create the categories/subfolders in WP File Download. Currently you can only import into an existing folder and must select the files to import individually.
Also, the option to log the import process to a CSV file where the original file name and location and the new file name and location are recorded. That way, if you're migrating a large number of documents from a previous website, you can add redirects for all the old links to the new document links. This would be especially helpful because all of the files get renamed when they're uploaded into WPFD.