I always forget that Nidoqueen and Nidorina can't breed for some... stupid reason but Nidoran female CAN!
I might be able to work this idea into something, it would be in chapter 1 so Jirachi wouldn't be available yet, I don't really want the MC making a wish with her anyway.
The scene could be a test set up by Maple to see just how fertile the MC is, if he can knock up the normally un-knock-upable Nidoqueen then it'll prove just how good he is