WMG / Pokémon Zeta and Omicron

The Super-Ninja Pokemon are illusions.

Which is why the Gym Leader doesn't use them. (and why the Ninja are literally invisible) They are the truth behind the "hallucinationary trainers" myth on Mt. Epsilon. The pokemon they use have a Gameplay Segregated Ability to tap into them. It requires hallucinogens found in the trees of the grove, though, so can't be used outside the Gym.