If it's configured properly, JIRA can be a fairly effective tool that mostly stays out of the way of developers but can help team leads and managers communicate things about the team.
Normally those issues would be handled with a simple 5 minute meeting (DSU or some variant thereof) where everyone shares their current state, and then a few times per month some form of "where are we and where are we going" type of planning. (Be it a sprint planning or something like it) Combining that with a state tracker seems like a fairly obvious thing to do, and having the tools to then report on that over time (graphs can be a helpful visualisation that simple tools usually lack) gives everyone some context as to how healthy the team is.
But even that last bit, the concept of periodically having a bit of a check up to see how things are going is often lacking in "we can do it better and simpler" types of setups. In then end, it gets reduced back to the manager walking around with a whip shouting "work harder!" instead of teams having some autonomy and figuring their own state out themselves.
This is why tools that don't allow this kind of doing-it-wrong are significantly superior to Jira.
Tools are just slaves to reality, not the other way around. If a legacy top-down organisation wants you do to a certain thing a certain way, and you have no recourse but to do as you're told, that's your organisation's fault and nothing else. You can either gain a position where you can make changes, or leave the company. Complaining about a tool that has no influence over your work process really doesn't change anything.
That's naive; tools influence the way they're used. When a tool defaults to having manager accounts that can change how things get done and developer accounts that can't, it nudges the organisation in that direction.
I think the core problem with Jira is organizations trying to use it to solve complex organization-wide problems. It is an enormous time sink, and using Jira to rule the workdays of employees is the problem.
Anything much more complicated than a checklist is wrong. Jira is an attractor for middle management growth that gives people who don't need to be doing anything something to do, and adding complexity gives more opportunities for more people to not do very much and generally get in the way of execution. It is also a way to give people who aren't very necessary or very good at understanding the big picture something that they can do to do.
Take away Jira and tools that you can order other people to use and you end up with middle management that literally doesn't know what to do because they couldn't organize or ease productivity to save their lives. Jira becomes the thing being managed instead of whatever is actually to be done.