I think that Jira killed Agile. It's such an overhead on the Agile process. Engineers spend more time documenting stuff in Jira than actually solving problems.
Jira is only a tool. You can use it for reasonable lightweight communication. Or you can use it as a basis for defensive posturing, preparing for financial change discussions and control freakish micromanagement. If you have a distributed team and can keep management out of it and stick to basic features Jira can help still today.
Agile is about culture and the culture of the pioneers and early adopters was different.
I‘m seriously thinking I should try to go more the Kanban direction these days to aboid the story point hitting / fitting in ever shrinking sprint trend.
Jira can be highly customized. I find it easy to use for day-to-day. I also have to deal with Jira with a subsidiary company, and their Jira is completely different, but it works well for their use case.
The reporting is a whole other issue. I don't use this, but my PM does because upper management keeps changing their reports and my PM has to keep linking and organizing. But as a developer, doing spring planning and burndown charts work quite nicely.