One of the great things about the WP Media Folder plugin, is that is uses a standard WordPress taxonomy to organize media. Unfortunately that taxonomy is invisible to other plugins that can be used to display images. There are tons of plugins that could make use of this taxonomy to produce lists of hyperlinked files, PDFs, custom galleries, etc. In particular Toolset Views and Types or PODS plugins would let users create sophisticated custom displays of media without hand-coding PHP in theme files.
This change could be set by default or you could add a plugin option to make the "'wpmf-category" visible or not, depending on user needs.
Other than that, this looks like a great product! Thanks.