The first problem is that everyone, even in the same team or org, needs something different from it. Sometimes it is even single individuals needing one particular thing one time, and the same day for another workflow or view another thing. It is when Jira caters to the wrong use case for you right now where the a lot of frustration arises.
In a similar vein, it wants to cater devs, coaches, POs, business people, customers and all of them over various orgs with drastically different workflows. Serving everyone equally must lead to a mediocre experience. You will always miss something, while there is so much stuff you don't need or want and you have to work around.
Arguably, this has become better a lot in the last 10 years, but you will always long for "something better".
But the most painful issue is that in some orgs Jira is the workflow, instead of supporting it and staying in the background. At some point people are only sending around ticket links, commenting on tickets, requesting people monitoring their queues. This creates overhead, redirection and Jira becomes a distraction you need to handle.
As a result Jira becomes a proxy for all the things going wrong with your daily work and a problem of its own.