Pokémon Ranger: Guardian Signs gives us Purple Eyes. Before we even learn he exists, he's beaten Rand within an inch of his life and kidnapped both his wife and daughter. Later, he beats the daughter up, too! It gets worse, though; he eventually mugs the elderly Societea members (though, admittedly, they deserve it), hijacks the villain's plans, makes himself immortal, pumps up Mewtwo's power higher than it should ever be, and then commands Mewtwo to finish off Dr. Edward. And when Rand takes the shot for Edward, Purple Eyes is simply amused and continues to attack anyway, even taunting Rand's daughter about it. After you beat him, he points out that the Sky Fortress is now plummeting and will wipe out all of Oblivia. And then he laughs. Rand's wife said that the ruins she and her daughter were captured and tortured in is the only place that gives her recurring nightmares. In the last Extra Mission, in which an enraged Arceus is passing judgment on the human race, he arrives in person. His imprisonment and constant questioning has not redeemed him, but instead turned him into a Misanthrope Supreme who no longer wishes to rule over all humans, but instead Kill All Humans. He begins preaching to Arceus that it should go through with the destruction, but to allow himself to act as its Dragon due to their similar beliefs about humans. This only enrages Arceus more. After you defeat and calm Arceus, Arceus leaves back to its home world and drags Purple Eyes with it, to pass judgment on him.
The Diamond and Pearl series gives us Pokemon Hunter J. As her name implies, she hunts rare Pokemon to sell on the black market, and has no qualms with stealing them from other trainers. She is willing to go to any length in order to capture these Pokemon for her clients, including attempted murder on her fellow humans. In her first appearance, she drops a section of her airship containing several of her own men, and the Pokemon that she’d stolen, just in order to be rid of our 10-year-old protagonist, who was in the same section of the ship. She shows absolutely no hesitation or remorse for this action, and Ash had only been a slight inconvenience to her at that point. In her follow-up appearances, she continued to demonstrate her sociopathic, greedy, ruthless nature, as well as her total disregard for any form of life by continuing to steal rare Pokemon, setting fire to a large section of densely populated forest in order to kill Ash, ordering her Salamance to attack humans directly, commanding her Drapion to squeeze the life out of Ash, and abandoning one of her clients to the police the second after she got paid. In the 800+ episodes of the Pokemon anime, she’s the only character who has proven to be purely evil with no redeeming qualities.
Grings Kodai, the antagonist of Pokémon: Zoroark: Master of Illusions. He kidnapped mother and child Pokémon from their homeland, imported them into another region, and blackmailed the mother into doing his bidding by threatening to kill the child. All of this is to cause the evacuation of a large city so he can find an energy cluster left behind by time-traveling Pokémon Celebi and absorb it, renewing his ability to see the future, which he acquired twenty years prior at the cost of annihilating the city's plant life. He's willing to destroy the city's ecosystem a second time, and why is he willing to do this? He's a wealthy and powerful businessman - he's doing it for the money.
He's got even worse traits than that. He forces Zoroark to allow him to obtain the Time Ripple by electrocuting her child right in front of her to the point that Zorua actually says he thinks he's going to die! Then, to make things worse, Kodai has his Pokémon try to kill Zoroark, since he's got Zorua in the palm of his hand and Zoroark is defenseless so long as he does, this means he does this for no reason except he CAN. He even goes so far as to say that he enjoyed doing it! And he manages to one up himself by trying to murder Zorua and Zoroark in cold blood when they trick him, despite the fact that he could've just went on ahead and ignored them to absorb the Time Ripple or flee (the latter of which Vicious and Pokémon Hunter J attempted when they were stopped). And he actually succeeded in killing Zoroark - though Celebi saved her, it doesn't change the fact that Kodai committed, thus far, the only successful cold-blooded murder of a Pokémon (all other times were accidental or just a side effect of what the villain was doing, but Kodai killed Zoroark intentionally, directly in front of the child she was in the middle of being reunited with!).
Charon was a money-obsessed Jerkass in the Pokémon games. But his method of introducing himself in Pokémon: Diamond and Pearl Adventure is to order his agents to suicide bomb a crowded stadium. Of course, it fails, but his intent is clear. He holds no regard for the lives of others and plans to control the world with money made from selling legendary Pokémon. Two of his organization's top officers leave to find the previous leader—Charon tries to kill them. Which becomes even worse when you find out that said previous leader is being held captive in Charon's base. And as a capper, that previous leader, who goes on to rally the remaining agents against Charon, had previously tried to destroy the universe.