I'm using GitHub Branch Source as an example, but this may apply to all Multibranch Pipelines.

Currently, I have hundreds of repos in a GitHub organization.   Many have Jenkinsfiles.  I have one that I want Jenkins to ignore, even though it has Jenkinsfiles (it's already built in another GitHub/Jenkins hierarchy).  Options:

1. Exclude Archived: I'd have to archive the repo, then I can't keep it up to date (it stores private tags)
2. Exclude Public:  This can probably work in my case, but it's an odd heuristic to remember.
3. Topics: an include-only filter.  I'd have to add the topic to all repos except one (and remember to do that for all new repos)
4. Filter by Name: I couldn't find a regex/wildcard that would work as an exclusion.  Same issue as Topics.
5. GitHub Team slug:  Maybe, but not any more obvious than "Exclude Public".

In short, I think that Topics and Filter by Name should have an Invert option.