I'm just thinking out of the box here :-), but there are a lot of generic Webmin modules that don't apply to the standard Virtualmin installation. These extra modules are somewhat confusing to uses not familiar with Webmin, especially when they conflict with built-in Virtualmin modules.
For example, Virtualmin supports Mailman, but Webmin has a Majordomo module. Virtualmin supports ProFTPd, but Webmin has a WU-FTP Server module. Virtualmin supports Dovecot, but Virtualmin has a Qmail module, etc.
It would be nice if these extra modules were automatically removed or disabled from view by the standard Virtualmin installation as to not confuse administrators. Perhaps this would require building a separate Webmin RPM just for Virtualmin, or perhaps Virtualmin could just have a config option to remove them somehow....