How about programming in the site creation script that would look for a directory in /root that could contain a "user-defined" site skeleton, and copy them onto each new site. A "site skeleton" would be defined as an optional set of files created by the host admin according to his idea of the standard site that wouldn't be overwritten by an ispConfig update.
When a site was setup, the script would look for the site skeleton directory, say /root/skeleton/ and if there were any directories or files there, it would copy them all into the new site with the same permissions and then chown them appropriately. If no directory existed, the script would just go on.
As little as a custom index.html page could be done, or cgi scripts, php info scripts, host policy and use pages, images.... as much or as little as the host admin wanted could be added on setup.