Whenever you fight one, you never get to attack. Ever. It flinches you, and then in the rare occasion you're not flinched, you get Parahaxed.
Make it stoooop.
I don't really think Jirachi overly affects the metagame, I mean Landorus and Heatran aren't overly uncommon and both aren't really that hurt by most of its common sets. I mean it's hax based but it's not like the hax depends on whether you miss or not because the hax doesn't affect you if it can actually be outsped and actually is by a lot of Pokemon. I'm also sure the scarf set isn't the most common. Also with the paralysis, it only affects you if you're slower, again, and idk, I don't really see it as something I'd be taking into great consideration of how to defeat when putting together a team.