I'm disappointed that you decided against exporting the stories as complete, stand-alone plugins.
An uninitiated user now has to install two plugins, load one of them, and then follow author-supplied instructions on how to import and run the story (choose Import/Export, choose the story in the plugins list, click "Import Lua", click "Main Menu", click "Reader", click "Load", click the plugin name, click "Select").
Whereas if you exported the stories as standalone plugins which included the reader source code (but not the Authoring and Import/Export code) all the user would have to do would be to load the story directly from the plugin manager. (This would also eliminate the problem of different stories being incompatible with different versions of Anthology.)
I think it will reduce the popularity of the system. Maybe not significantly, but somewhat.