It's been over 10 years since I last used Jira, but I still miss a lot of it. Where I saw it become a problem was that over time it accumulated layers and layers of people messing with it, especially as the company went through a phase of hiring project managers with a need to mark their territory by changing all of the workflows. What started out as a relatively lightweight tool used by the engineers to organize their work became a convoluted mess.

To be fair, that's not unique to Jira, and I certainly can't say I haven't put my own fingers in that pie.