Though, Miyazaki's personal favorite would have to be the hospital bombing scene, because it brought the character of the Joker full circle, with Arthur being made to leave the hospital to the Joker blowing it up.
Author's note: No worries guys, a gym doesn't mean he will sit in it all day. He will make trips across the world for new pokémon, or other advantages from metaknowledge. Think of an expedition of Mega stones, or for Moss rocks.