Jirachi needs to be awake to do big wishes, that only happens when she's been asleep long enough, if Jirachi charged her up she'd just sleep run around the ship granting small wishes all over the place!
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She'd be granting her own wishes for everyone else, regardless of if they want them granted or not.
Like she'd wish that Lugia's ass would always be bouncing and then sprint off again, leaving Lugia complaining that she can hardly walk due to all that jiggle going on behind her.
I've got a good idea how to end the scene too, but that'll stay secret until it's written