I think one of the big issues with JIRA is that it's configurable enough to be a project management tool. It's a really great issue tracker (IMO), and I think when you aim to use it as more than that (involve proper releases, milestones, scheduling/time-tracking, etc.), all of a sudden you get into the areas where the configuration and education issues that you mentioned become apparent.
Project management software is difficult, you either have a mess of features that don't work well without customization, or you have few features, and force teams to model their workflow around your features.
In the context of this post and the greater bitbucket vs github discussion - do you find GitHub issues to be better than JIRA?
Re: JIRA. At work we've been using Jira for several years. While it's very flexible, it does come with a certain level of complexity that makes doing things like simple Kanban heavier than it should/needs to be. I have a billion opinions about JIRA, and a love/hate relationship with it.
Github issues - bare bone basics, but I hear they're working on improving it. You cannot currently run something like a Kanban board off of GH issues without outside assistance.
For simplicity, boards like Trello and AgileZen are, IMHO, in the lead.
I have a billion opinions about JIRA in general, but I doubt anyone is interested besides Atlassian. ;)
My own experience with Jira is that it's easy to misconfigure when you start, then later on there's too much inertia in the userbase to fix it. I liked it, but you have to know it a little before you use it.
Project management software is difficult, you either have a mess of features that don't work well without customization, or you have few features, and force teams to model their workflow around your features.
In the context of this post and the greater bitbucket vs github discussion - do you find GitHub issues to be better than JIRA?