We at GitLab are trying to keep it simple by having only one repository, one wiki, one issue tracker, one CD pipeline, and one set of milestones per project. Projects always below to a group. We aggregate on the group level, for example issues https://gitlab.com/groups/gitlab-org/issues, merge requests https://gitlab.com/groups/gitlab-org/merge_requests and milestones https://docs.gitlab.com/ce/workflow/milestones.html#groups-a...
There are several things we're still considering to solve this problem better, comments are very welcome:
1. Multi project pipelines https://gitlab.com/gitlab-org/gitlab-ce/issues/17069
2. Group level issue boards https://gitlab.com/gitlab-org/gitlab-ee/issues/928
3. Nested groups https://gitlab.com/gitlab-org/gitlab-ce/issues/2772