A powerful tool we currently have available is the Desktop Client. With it, you can mass move and organize your files (using copy/cut/paste or drag-and-drop), as well as create new Folders within existing Folder Channels, or move/copy/delete existing Folders. One limitation is that you cannot create new Folder Channels (but you can create and organize content within those channels).
Besides the Desktop Client, this feature has been logged as a Feature Enhancement with an id of ID18226304. You can receive updates on features by following our product news blog. If you would like, I can add your organization to the list of requesters for this feature.
Hope this helps,