Makes me wonder how some polls would turn out if options had both upvote and downvote buttons. I have used every bug tracker in this poll, as well as a few more (redmine, Assembla, GNATS, OTRS, Roundup, ikiwiki, various custom internal tools), and Jira was by far the second worst (behind one of the custom one-offs).
Depends on the situation, and how it is being used.
It does take a serious amount of time to set up, but it is so flexible that if you take the time, you will never leave it.
It also integrates into everything, and has a very verbose API, so if it doesnt do what you want you can extend it.
I'm surprised. Our company evaluated several bugtrackers and jira was by far the best. We're still using it two years later and still quite happy with it.
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.
I didn't have a very high opinion of Jira until about version 4. In recent updates, a lot of the clunkiness of older versions seems to have been cleaned up.
Until recently, my team was the only developer group in our company using an issue tracker. Management have decided that every team must now use an issue tracker and that tracker must be HP Quality Center. They're even paying a temp to manually migrate all our Jira issues into QC. We managed to win the battle for Git over IBM Rational ClearCase for a version control system but this kind of thing makes me think it's about time to find a new job.
Being one of the engineers actually using it on a daily basis, all I can say is: I don't know why you have the impression that that is the way you need to use the product in practice, but that certainly doesn't match our experience. We hardly use the workflow and reporting components and you really don't need to, to make good use of it. And we're quite happy with Greenhopper as well. It's far from perfect, but Greenhopper is useful to us, where all other project planner / issue tracker crossovers were found to be borderline useless for our use cases.