After being forced to switch from Jira to a much less capable system, I now wish nobody had complained about Jira. Grass is always greener.
For my personal projects I use JIRA server (solely because its cheap at $10 and has a decent mobile app to capture ideas in tickets/boards on the move) and my experience has been pretty good.
That being said if Github had a good mobile app I'd switch in a minute. My main problem with Github issues is that you cannot edit milestones in the mobile web app.