I'm using Zenhub at my current company. I preferred Pivotal Tracker, which we used at my last company. It just feels kind of janky overloading Github's website.
TBH, though, I struggle to find any other meaningful negative differences.
We use JIRA at work, and there are good and bad aspects.
My biggest peeve is that management always want to configure it to do time-tracking. This makes engineers hate the tool and lie to it, making it useless for bug tracking.
TBH, though, I struggle to find any other meaningful negative differences.