If a job needs to exist purely to maintain a third party tool that you pay for, you probably should find a new tool or make the tool yourself so that the employees work value is retained. It's the equivalent of doing a complete kitchen renovation on an apartment that you rent.
Jira is not perfect. But the atlassian suite as a whole, with integration between CI, PM and version control, is quite powerful and more than adequate in many cases.
That said, boy have I seen it used terribly. It's double edged for sure.
If you have a team to manage it then you may as well use that team to write your own, then you truly get the flexibility with none of the performance downside and having to program in crappy languages with crappy tools. Plus it can grow and evolve with your organization, for a start up a couple of cgi scripts on a rasberry pi are enough, for a large enterprise those cgi scripts are probably still 10 times faster than JIRA.
JIRA has become the SAP of bug of issue trackers and no one can use it well out of the box.
What we need is Jira and Trello to have a baby