Jira has implemented all those features because that's what the industry (managers and people that like control) wanted Agile to become, so, to make money they did so. I don't blame them for that, they aren't the defenders of Agile. Again, the problem isn't Jira.
If you strip away all the reporting, burn down charts etc what you are left with is an exceptionally powerful Kanban board with, in my opinion, a solid user experience.