We have solved this in Deveo by grouping repositories inside projects since it reflects more naturally how software is built outside the open source community. This has been our focus from the inception. In non-open-source projects, a project typically includes multiple repositories (such as backend and frontend at least), and they all share the same issue tracking and wiki functionalities.

We covered this topic and other differences between Deveo, GitLab and Bitbucket recently in a blog post. If you are interested to see an alternative viewpoint on things, check http://blog.deveo.com/what-makes-deveo-different-from-github... - I would love to hear feedback whether our approach is viable compared to GitHub's open-source approach on things.

Disclaimer: I work at Deveo