I had a similar thought: Jira is very customizable; if people hate something that is so customizable then part of what they're hating is the organizations customization of it.

I've seen the same thing at multiple companies. Someone comes up with a Jira workflow, it doesn't match the needs of some people, but the company wants to standardize on that workflow, so now people are stuck using a stupid workflow that doesn't work for them. I've also seen a bunch of stupid custom fields on every single ticket. Is this Jira's fault or the organization's fault? You complain but the word from your immediate manager is that the team is already in hot water so escalating complaints about the Jira configuration isn't going to help, etc.