The biggest problem I have, by far, is just how easy it is to create bureaucracy-intense workflows in JIRA and make management believe these are absolutely necessary. Most developers do not need this info, and do not have the power to easily change things. All the fields when making a simple ticket, the dozens of sub-tasks, the ticket inside a ticket inside a ticket. I would believe this is not impossible to avoid, but I do feel a simpler structure using labels, milestones and issue tracker is far, far easier and less prone to being misused. GitLab and Github can both do this as far as I know.