Right now, my team uses Jira for tracking bugs and features and whatnot in our custom software development. We also use it for tracking issues and work related to our infrastructure, access requests to our various data centers, budget requests from the team, software and change management planning, site audits, and probably a couple other things I'm forgetting off the top of my head. And yes, there are likely better products for each of those things individually, but then you wind up in the hell of "oh wait, audits go over here in Freebly, but software releases are over there in FrobniTZr", and if you run those tools it's suddenly fifty-leven more hosts and apps to support and keep patched.
Much like Excel, Jira might not be the best tool for all our use cases, but it's pretty good at several of them and good enough at the rest that having everything in one bucket outweighs the potential benefits of a better tool.
On the other hand, if someone would like to fire up a start-up to develop a similarly flexible on-premises work management product to replace it, you'll absolutely find me in line with my wallet open...
Also, it is not that great.