Here's a list of settings and features for GitHub projects that I've found recommendable to pretty much every project. Some of them would be nice to be on by default by GitHub so new projects would have them right out of the box, but while they are not, here we go, in no particular order:
Even if the project is not written in a supported language, GitHub Actions workflows are used by most. CodeQL supports checking them, which makes them a nice lowest common denominator.
In my typical workflows, the most important aspect of auto-merges is to be able to enable them while workflows are running, as they may take some time. This requires setting up branch protection rules to require some status checks. This is fine, but it's a chore that one needs to select every single status check (~ workflow job) separately and mark it as required and remember to update the list whenever workflow jobs come and go; there's no option to just "require all things that run for a PR to pass" (as of 2025-07-18).
PR branches are rarely used for anything after merged.