Nice-looking URLs for assets
Perhaps using redirects and Regex in your .htaccess? There's a Craft plugin that would help with this.
https://github.com/rkingon/Craft-Plugin--Redirect-Manager/

You could use something like:

RedirectMatch 301 /download/(.*) /several/subfolders/for/organisation/purposes/$1 


You would need to refine this for matching several different subfolders.