If you run Jira, Confluence and Bitbucket, the level of integration you can achieve is pretty unmatched. The cost: You need to buy the data center edition, on-prem is required to get any sensible level of performance, and you need Atlassian experts on staff.
In the few different companies of different sizes that I worked, I never saw a Jira that did not become a hot mess until people start new projects or new boards when they can't bear anymore.
I find it also extremely difficult to find anything. Like you know that an issue exist but search will not help you find it easily. Very often I have to go to Gmail to search in notifications to find back the link to an issue.
In our company our CIO declared everything should be agile. So now we log our hours in Jira. That's it :P supposedly that makes us agile or something.
But yeah the VP they acquired from another company to manage us is a total tool.
Perhaps you've been fortunate enough to be employed where these things are managed better than my hypothetical scenario above, but my experience that is the exception, not the rule, so it's not surprising that people can become fatigued.
There's no obligation to propose a better solution when saying something sucks.
It can look a little bit rough, and sure there could be lot of improvement. But it favored efficiency against eye candy design.
It is very easy to have things organized the old way. Having projects, recursive sub-projects.
You can look at your issues at the sub sub project level or at a more global level.
You can easily have list with all the variable that matters. That you can order easily how you need: Who's the rapporter? Who's the dev? Who's assigned to? What is the state? When was the issue discovered? In which version? Fixed with which milestone?
It is very slick, I did not feel a latency like in Jira, the screen is not filled with useless crux, only what matters fills the screen. In a few clicks I was always able to find what I was looking for, set and identify all the affected versions and which one got the fixes.