It would be useful for certain features, like giving Pokemon with custom, unique, or egg moves as rewards or events, recreation for giving or battling Pokemon with specific moves, or ensuring Pokemon you encounter in story-mode content isn't able to kill itself with certain moves in its move pool (Uxie Memento, as an example).
Items would also be useful as a Pokemon Spec, also as rewards, events or recreation, such as giving a mythical Pokemon holding a golden bottle cap, like main game events. Or giving a player a Pokemon that is battle-ready with a Mega Stone, maybe in the format of /pokegive Lucario HeldItem:"pixelmon:lucarionite"