1. People already have accounts, so it lowers the barrier to reporting issues and contributing.

2. GitHub provides some level of discovery that's hard to replicate otherwise.

Both of these are a function of GitHub being popular. It doesn't have to be a particularly great tool if it's what people are already familiar with. I wish it were otherwise, but I don't see a real alternative that can compensate for these advantages in the short term.

I love your idea of having issues/discussions/etc managed directly in Git—that seems like a more flexible and adaptable system. Even if somebody developed a standard like that, though, it seems impossible to get any of the big repo hosting sites to adopt it since it directly competes with their own value proposition :(.