>>56526209voltorb and electrode's wood carapace became infested by insects, causing them to explode before they could reproduce, only the electrode with more metallic shells passed on their genes
zoroark was too violent and kept killing too many people, leading to people hunting it to extinction
goodra's shell was too heavy, and it was poached for the rare ore, leading to shell-less goodra surviving an passing on their genes instead (see elephants)
enamorus is a legendary pokemon, she could simply be on the other side of the earth in the century that DPP takes place