Cats and Horses are extinct in lore so they're a no go.
Legion: Cazadores with a "keeper" using pheromones to control them(ala Queen style)
Legion: (just because adding more to them) since they only use "natural" healing etc (healing herbs and powder) how about the spore people with Legion. A mutation due to overdoses of the healing herbs mixed with radiation and a genetic defect. It'll give more uses for those creatures.
Bighorners in place of horses for chariots etc would be good.
Maybe use the Minotaur and spore people with the Aliens as well as their abominations. Alien experiments.
Outcasts: any and all type of bot. Cyberdog.
Enclave: you've got covered
Somewhat of topic but. Ultimate Enclave experimental pet. Behemoth fully armored with the Reaver nuke grenades and glow. Mega boss.