This is the example of how hard it can be for companies, especially successful companies, to alter their course even slightly.
Github success was about making code repositories pretty and social. But this is no longer enough to keep evolving as a company of their size. Yet the internal product DNA still revolves around repos, so as a result, issues, wikis and now Projects (!) live under a single repository.
This is backward.
A project is a way to group resources to achieve a predefined goal. Those resources include multiple people, multiple issues and multiple repositories. Sticking a project under a repository makes no sense.
In fact, a code repository in most organizations is a fairly small and an insignificant asset, just another way to organize code, i.e. function -> module -> directory -> repository, etc. It's quite awkward to think of what your company is doing in terms of repositories, so anything Github adds to repos feels out of place by default.
Another example of repository-centric thinking is the homepage of https://github.com itself when a user is logged in. It's the most important page of all, yet nothing on it has any relevance to me: just a list of people I like starring random repos. Same thing for the organization home page, just a list of repos, again.
The Project idea is great. It had the potential to solve all of these issues by giving me a tool to organize digital assets in a way that's important to me. But sticking it under a repository killed it.
[EDIT] It's easy to be me and be posting a comment like this, telling successful people what to do. But it's enormously hard to have a large team of PMs, developers and designers, all of whom are smart and ambitious individuals, to actually do something that falls outside of the settled way of doing things. Kudos to Github founders and employees for getting it this far and congratulations on dealing with big company problems ;)