The reason that Jirachi is good is that you can use it to grab any supporter in your deck. Which means any poke ball that can grab Jirachi also turns into any supporter. Skyla just lets you grab any trainer card, but if you grab a supporter you can't use it that turn. With Jirachi you can.
Think of it like this. If you have 1 of team mates in your deck. With Jirachi and 4 Ultra balls. You can get Teammates 6 ways. By drawing it, by drawing Jirachi and then searching for it. By drawing an ultra ball and then searching for jirachi, and then searching for teammates.
This works for any of your supporters. Making the deck much more consistent.
This also means that if you are drawing dead and are going to lose for certain. Drawing into one of your ultra balls can turn into the Sycamore that can get you out of the dead hand. Turning a certain loss into a chance for victory.
If you are worried about the 90 hp. So what? if they choose to target down your Jirachi, that means they are leaving your attackers alone, thus allowing you to revenge kill their attackers.
Only time it becomes a real problem is if you are at only 2 prizes left. But if you didn't play Jirachi earlier, you would have lost anyway.