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Great comment, and I'm glad you replied with these examples. The problems you describe are corporate software development process problems and not problems with Jira or bug trackers in general. It's a dysfunctional company welding their dysfunction onto Jira, and Jira gets the bad rap. Most of the time when people on HN complain "I hate Jira!" what they really mean is "I hate my company's inflexible software developm…
The problem with company C style work is when you do really small incremental changes. I have had 40+ commits for a single issue, being very gradually rolled out. The time taken to manage tickets in that case would easily have exceeded the time spent on the task itself.
If JIRA is not a good fit to this model, too bad, that's JIRAs problem. Don't make you dev process worse to appease JIRA.