Jira seems like the kind of system sold to managers and then inflicted on engineers. Managers love it because, like Excel, it's the kind of tool that lets you easily generate reports and enforce workflows without programming. (And in fairness, that
can be a major selling point.) However, from an engineering perspective, it makes simple tasks clunky; it turns what should be 1-2 step processes into 5-step processes, and otherwise manages to be the antithesis of a lightweight tracking tool. The phrase "makes the difficult things easy and the easy things difficult" (or "painful") comes to mind. In particular, the tasks it makes difficult/painful are the ones that engineers find themselves doing 30 times a day.
And for agile/scrum, Greenhopper is absurdly bad, for the same reason.