JIRA is really an amazing change management tool, and the cost is not bad as these tools go.
Developer Focus
The only thing that has been the downside (and maybe the upside of JIRA marketwise) is that its very developer focused. They´re interconnections with the other devtools they offer including Fisheye, Bamboo and others are simple and very very functional (combine that and you get functional oO).
Atlassians Agile Plugin Greenhopper costs as much as the tool it self, but is mindbogglingly good. Virtual wallboards, drag and drop, prioritizing/ranking, and configurable for scrum agile, "scrum but" .... ohh my.
User Interface
Lately they have upgraded the UI and made it much more user friendly. They still have some stuff to fix, maybe I should lend them my User experience designer, but alas I can´t spare him ;).
For Testers
Testing wise they have made HUGE steps forward, lately it was the Atlassian JIRA Bonefire which looks to be amazing.
But .. Project & Release Management ..
They big thing they are missing, are huge steps forward in Project & Release Management. Nowdays everyone is "Agile" whether they really are or not. That means small projects, or at least big project split in small parts. Now then you need to be able to handle that well. And yes they have made some steps in that direction. For example being able to tag an issue to multiple versions (that is what Atlassian calls the releases of a project) is good. But it´s an workaround really. Using the concepts you have but in a bit better way.
I hope that Atlassian turns their attention to Project & Release Management a bit, to have Improvements like Create versions on multiple projects open since 18/Nov/03 11:14 AM shows that Project & Release Management needs more focus and effort.
At my work we release once a month, that includes ALL projects, small improvements (in the "improvements" project if there is no project running that they can conveniently be smuggled into) and maintenance. Very lean and agile and all that, works very well. Business is happy, developers are happy. Testers and Project Managers could be a bit more happy. Keeping it all together can be a pain and I won´t mention how much a pain in the butt the release notes are.
Just my 2c
/The mountain troll