* block trolls from interacting with an organization, short of filing a support ticket
* install pre-receive hooks without using the pull request infrastructure
* set up status checks (the PR equivalent of pre-receive hooks) for pull requests that require force pushes, allowing some external check to replace git's usual fast-forward check
* have status checks apply to individual commits, not trees, so that you have style or copyright or whatever checks on each commit
* disable pull requests
* enforce rules for creation of new branches or tags
I admit that none of these features are dealbreakers, but they all have legitimate use cases, and they'd all be trivial if you were using a regular UNIX-based git server.
On the other hand, the usable interface of GitHub wouldn't be available to you if you were using a regular UNIX-based git server, and that is a dealbreaker. :)