Can you please elaborate on this configuration? What is the general nature of the configuration changes you're making? Or, how is your workflow affecting the product. I ask as I am in an organization right on the cusp of implementing JIRA, and I would love to steer the implementation team toward a more useful configuration than the clunky defaults, with which I've had prior experience.
* Setting up several statuses (more than in the default) to reflect backlog, selected, in progress, testing, deployed
* Creating an appropriate board which splits everything into columns by status and rows by user
* Setting up a few quick filters to find things like anything which has been in the backlog for more than 6 weeks or bugs which haven't seen activity in the last 48 hours
* Integrating GitHub. Being able to kick a ticket over to QA from your commit message is awesome.
Beyond that, I mostly focus on stripping out default things to make the workflow simpler. I don't need my software to enforce that I can't move a ticket to deployed straight from in progress, and stripping out those extra rules makes it easier to deal with.
Issue trackers are like utilities, like electricity and water. If they're doing their job, they're invisible. You only notice them when they're broken.
As a result, all issue trackers have more detractors than promotors, with the vast majority of users being neutral.
That said, I've used RT (holy shit no), Pivotal Tracker (drinks too heavily from the dynamic DOM/JS koolaid, sucking up all RAM and CPU in the known universe), and JIRA. I'd take JIRA over the others.
I've used Mantis and Bugzilla and I'd also take JIRA over those.
JIRA is the best bug tracking software I've used since I left Microsoft, which was over a decade ago. Sometimes I still miss Raid, particularly it's ability to build complex queries, but also the ability to connect to any team's project. At the time, it was supposedly the only internal tool used throughout the entire company.
With just a little tweaking (30 minutes or so on a fresh install), I can have it perfectly configured to match my ideal workflow.