I think the UX and design of Jira and the rest of the Atlassian tools is pretty good. It's reasonably clean and consistent while being customisable as required.
If anything, I'd use Jira as an example of what enterprise software should be like! It's hardly perfect, but I s better than almost every other non-tech-oriented SaaS I've used.
I think it's the enterprisey configurability really. A lot of the instances I've had to use were confusing messes with local OK parts, I wouldn't be surprised if some combination of configuration yielded much better usability.
Bugzilla is obviously very ugly (and directly out of the 1990s) but it does work pretty well and it's fairly logical to use.
When JIRA started it was beautiful when compared to other available options (bugzilla, for example). JIRA's UI was a major competitive advantage in the beginning. These days, it looks and feels terrible, IMHO.
