I'm not so sure managing issues is a non-existent problem for large projects. For example, Canonical have Launchpad (also used by Mozilla, MySQL, a bunch of other distros etc.), Django have a custom issues tracker, etc. I don't know if waffle.io is it, but these examples suggest that perhaps there is a point where something is needed beyond Github issues. On the other hand Rails seem to use Github issues alone so maybe you're right.