The main way I've found this to be annoying is GitHub "Deploy Keys"[1]. They treat them similar to users, so you need a unique deploy key per repository. That is pretty annoying when trying to authenticate something like a CI server.
The main alternative is "Machine Users"[1], which are actually normal user accounts. That means they have the same policies as regular users, like mandated 2FA for an organization. And to manage them you have to log-in as that user. That makes it a pain for a team to manage a Machine User.
GitHub really needs to have Service Accounts that belong to an organization, and can be managed by admins of the organization (without having to log-in as the Service Account). The Service Accounts should be able to have SSH keys and API tokens associated with them.
The main alternative is "Machine Users"[1], which are actually normal user accounts. That means they have the same policies as regular users, like mandated 2FA for an organization. And to manage them you have to log-in as that user. That makes it a pain for a team to manage a Machine User.
GitHub really needs to have Service Accounts that belong to an organization, and can be managed by admins of the organization (without having to log-in as the Service Account). The Service Accounts should be able to have SSH keys and API tokens associated with them.
[1] https://developer.github.com/v3/guides/managing-deploy-keys/