Generally, it's an issue of the media upload UI, not a backend issue. Big question is how to distinguish between uploading a new version and uploading a thumbnail.
Do you think it might make sense to auto-generate thumbnails for some set of recognized formats? Each upload would not only create a new version, but also a set of thumbnails for that version.
Right now, all of the thumbs are automatically generated for images. I'd like to add feature to do this for PDF ... and to make it easy to get the thumbnail of a revision.
If we want more control over the thumbnail, maybe it should just be the "Featured Image" for the 'document' post type??
I also think this would be an excellent idea. We'll be using the plugin to host reference projects, where we'll upload a zip with multiple files. Often the projects are design related and it'd be very useful to be able to upload a thumbnail for reference.
We're using it for internal purposes, so for us it would be important that the thumbnail gets the same status as the document, i.e. if document is set to private, the thumbnail will also be set to private.