I'm right there with you on Jira. The haters are wrong - it's a decent enough ticket system, no worse than anything else I've used. You can definitely torture Jira into something horrible, but that's not Jira's fault. Bad managers will ruin any ticket system if they have the customization tools to do so.
Yeah, usually Jira hate is really convoluted company process hate. Of course the Jira software isn't perfect, but it's fine. Jira's strength and weakness is it's flexibility.