Rare but not very rare if you are in Japan.
In Japan there has been a shiny Jirachi event that started December first 2014 and ended May 28 2015. So in Japan you most likely have a Jirachi if you have gotten the game before May 28 2015. However, since the event is only available to Japanese, a shiny Jirachi is rare for thee rest of the world.
Hope I helped!