Jira is an incredibly flexible business process tool that - among other areas - lends itself particularly well to software development processes in larger organisations.

With all the criticism levelled against it I have yet to see a better tool of this kind.

Jira isn’t opinionated about the process that’s implemented with it. If you want that there are alternatives such as Basecamp for instance. If you want something simple there’s always GitHub Issues (or similar tools).

If you need something customised then other than building a tool yourself Jira likely is your best alternative (unless you want to manage your process with Excel sheets, that is ...).

If, on the other hand, your process is broken and built around anti-patterns then yes, Jira will absolutely help with fostering and perpetuating those but it’s really not the tool that’s to blame in that case.