Jira is an amazing argument for the idea that having too many features is itself an anti-feature, and github issues' second biggest strength compared to it (behind the integration with github) is specifically that it doesn't try to do everything.
Or an argument for doing it right. It's got a query language that looks a bit like SQL, just... not SQL. It's got an ugly but responsive UI. It's easy to over-customize.
The real problem is that it gets over-customized, and as with all databases, schema is forever, so after enough years of using it you have: ugly remnants of how you used to do things mixed with the ugly new things you're doing, and a devops team dedicated to maintaining and further over-over-customizing your JIRA instance.
