>>54162394IIRC they didn't want to make the Mother Beast a Pokémon because then you could have the player controlling humans. Which might be related.
There's definite leftovers of an earlier concept where Z Crystals were used to trigger some kind of forme change rather than an attack.
Crazily enough, they have the same shape as the gimmick items from that weird manga that humans can use to fuse with Pokémon. And they also made the odd decision of putting Ash-Greninja into the game.