Classic JIRA is very flexible into shaping a workflow, but it's sort of a very long pipeline of: schemas, fields, workflows, project templates, etc. I loved that flexibility and being able to drill down into a bug report, but it definitely took time to set up, and occasionally unravel & put back together when you needed to fix something small.
There's also the usual stuff of finding & setting up plugins, and then looking for a maintenance window that people can agree on, while side-stepping those settings you forgot needed a restart to apply (thus bringing your live maintenance to a halt because you can't bring it offline now).
Running core versions of the products aren't terrible - usually the complexity comes with the slough of plugins that folks install to customize the platform, all needing to stay up-to-date.
There's also the usual stuff of finding & setting up plugins, and then looking for a maintenance window that people can agree on, while side-stepping those settings you forgot needed a restart to apply (thus bringing your live maintenance to a halt because you can't bring it offline now).