The problem with JIRA is the culture that it encodes and enables. It's rooted in the belief that programmers are factory line workers who aren't smart or organised enough to keep track of their own work, so invariably control of it gets assigned to a "project manager" who then spends far, far too much time engaged in busywork. You end up with hard-coded workflows that don't match how people actually work and the people who need to actually
use the workflow get frustrated.
Fundamentally JIRA is an over-grown bug tracker. A bug tracker should be designed, built, administered and used by programmers and only programmers. Project managers should not even have access to it, in my view, let alone try to use it to create reports or control the team.
Typical problem I face in my JIRA shop: there'll be no way to move a task straight from "to do" to "done". You have to move it to "in progress" then "in review" then "in qa" then "done", even if in fact, the ticket just tracked the need to do a quick code cleanup that happened to get done as part of some other task. There's no justification for this type of thing beyond over-empowered project managers.
