One side thing that I did want to touch upon was their use of their Ionitron bot to handle "dicey" situations when dealing with other users. Is it really that big of deal telling folks on the internet potentially bad news? So their Pull Request was denied/closed for some reason. Who the hell cares if they throw a temper tantrum? They're nothing more than a username on the Web to the rest of us. As long as the maintainers act with poise and integrity (and I've no reason to think that the Ionic team doesn't do that already) then they'll only be looked at in a favorable light.
Github is under a lot of scrutiny right now, the community is waiting for the response (which doesn't seem to be coming).
It's a good thing to see that you can work around some of the limitations and that people are actually doing it successfully.
There is a vocal minority that is looking for more powerful tools to manage their specific project's workflows, often related directly to the behavior of their audience, which sounds like an obvious opportunity for custom tools (to a software developer at least).
For many projects, the structure and interface third parties provide is almost always worth leveraging. Get 99% of your product from day one and spend your time hacking on the few additional features you may need.