Having to create issues-only repositories seems like a sign that one may be using the wrong tool. But the simplicity of GitHub Issues, and the fact that most issues on my plate are related to a particular repo, makes it tempting.
You don't really need this, though. Github has a project board, too, and it's ... pretty good!
My gig is still in Trello-land and I'd like to move away from it but companies have a tendency to include biz folks in Trello whereas Github is scary tech world to a lot of them.
Worth checking out the new GitHub Issues beta: https://github.com/features/issues/