Parent site template which can push changes down to previously created sub-sites (similar to list/library parent content types)
Many customers use a site template to create project/program sites in their environment. Generally speaking the lists and libraries that are in the site template are composed of content types so that changes can be made in one place and easily pushed out to all locations using that content type. The one area where SP is lacking is in the ability to easily push out changes at the site level to all the sub-sites where a certain site template has been used (e.g. change the navigation, add a new list, create a new page with a few web-parts, etc.... then push those changes to the many project/program sub-sites so you don't have to do them all individually).
Jeremy Caney commented
This would be really useful, especially for large deployments.
One of the best practices we preach to our clients is to establish centralized master templates, list templates, content types, and, where appropriate, web parts up-front so it's easier to manage (and cross-reference) content later.
We also use site templates for this. But the inability to inherit changes to those templates after site has been provisioned greatly limits their usefulness. Ideally, sites would have the option to continue inheriting changes from the site definition, web template, or project solution they were created with so that themes, features, web parts, and other configuration settings could be easily rolled out to a large number of subsites later on.