Just like JIRA has "schemes", I'd like to be able to apply a group of settings to a repository.
For example, we have about 250 repositories and only about 3 different workflows. Each workflow involves settings ranging from branch permissions to the settings for a number of plugins. In total we need to configure about 20 settings across various different pages. So if we take 5 seconds per setting then it takes 7hrs of configuration effort to set up the repositories. Then if we discover an enhanced workflow we have to open up all the repositories in tabs again to do it over again.
I would suggest having a way to have a setting profile that you can select per repository. For ease of dealing with custom repository settings it could be such that if you have a profile selected it uses it and disables repo settings, otherwise you can ignore the central profile and configure the repository yourself. Alternatives there include more selective overrides at the repo level.
This same thought about global configuration profiles applies to projects as well, but the biggest pain point is repos since they have the majority of the settings and they are nested. We have even been building an internal tool to attempt to deal with this problem ourselves, but my dev indicates that some settings (such as for the Workzone plugin) don't seem accessible via REST (not confirmed).