It's been discussed here already. First off Charizard was not in the intro to Sinnoh League Victors which could be a hint that it will not be used. Second, Charizard didn't appear in the Hoenn League which means that he has not made an appearance in every league match. And lastly, Sinnoh is pretty far away from Johto. I think it is too far for Charizard to fly there (ofcourse they could transport the pokeball but they have never done that before).