That said, a good TPM is often worth more than a good engineer. Herding all the cats across multiple teams, projects, competing priorities, keeping track of stuff, holding and being held accountable. And part of a good TPM is to find the right way to work. Maybe it's Kanban. Maybe it's Scrum. Maybe it's Waterfall. Maybe it's a mixture of different methodologies, like waterboarding.
That was the whole point of "Individuals and interactions over processes and tools", finding the right way to work for your team. Jira has to deal with the fact that it's meant to be a tool that fits into any company, so it's generic/customizable, and I've seen too many teams go crazy on the customization, trying to model out a massively complicated process when the team really just needs Kanban with a few extra fields.
I don't hate Jira - I don't like it very much, but I acknowledge that a lot of Jira's issues boil down to mediocre PMs being in charge of it.
Having worked with a good TPM that can really make things happen was eye-opening - tools like Jira can work beautifully if they are setup properly.