As a person using Jira daily in a, fortunately well done, agile environment. I must say I can see how, when used with all the bells and whistles, strictly-enforced-workflow this and work-log that, it would be unbearable, the worst interpretation of Agile used to justify creating a sacrosanct "process" and going against the very core "people over process".
As a bug-tracker shoehorned into doing double duty as a Kanban board, does Jira have rough edges? Sure.
However, used as a slightly more feature-full variant of Trello, as a wall of virtual sticky-notes, as a way to help see if the team improves over time like it should, it's pretty useful.
The moment it becomes an impediment it, well, is an impediment, and should be dealt with accordingly.
As a bug-tracker shoehorned into doing double duty as a Kanban board, does Jira have rough edges? Sure.
However, used as a slightly more feature-full variant of Trello, as a wall of virtual sticky-notes, as a way to help see if the team improves over time like it should, it's pretty useful.
The moment it becomes an impediment it, well, is an impediment, and should be dealt with accordingly.