Although there will still be lots of projects (e.g. `an open source project with one repo`, `some company with a huge monolithic repo`) that will be able to use per-repo Projects profitably.
But yes, someone, please make something that kills JIRA as soon as possible.
I think they could iterate on this to a place where projects are repository-specific, but still useful for high-level organization and planning.
For example, if they allowed repo projects to reference issues in other repos, that would you get you 99% of the way there. You could start a single meta-repository that referenced as many repo-specific issues as you cared to consider.
But yes, someone, please make something that kills JIRA as soon as possible.