Spoilers ? In one of the data research thing , it is said that Nihilego is a parasite . What parasites do is that they take control over the host , in this case Lusamine . It is smart of Nihilego to use pokemon to fight instead of LusamineNihilego because of the damage Nihilego and Lusamine would have to go through , possible killingwounding them since the combination makes them part human . This would end up with Nihilego losing its host which is the most important thing to parasites . Just my thoughts . Also , technically they are not pokemon because of the aura they have and their facial expressions changed , so this probably means Nihilego infected them too . EDIT Had to change a few words and add some more stuff . Plus , Nihilego had to possess Lusamine to strengthen her pokemon . Maybe turn them into UBs ?