This suggestion came to my mind just now... Say for example you are trying to sort out the inventory of your rhyhorn, but the rhyhorn is still mining the stone/ore got from the geos, you disable his operations via the Pokemons main menu and continue to sort his inventory, the end. How about that? That way you don't have to replace your Pokemon for when you are doing something that relates to your Pokemon's operations!
Brilliant idea. It will really help players sort items out or move their pokemons. Maybe if there was a sorting system too,those two would fit perfectly.