Do you think the people of the pokemon universe consider Yveltal and other destructive pokemon evil? Affection for legendary pokemon works the same way it does for others, should we have to earn their trust in a different way? And they still do things like play minigames with you and make cute faces when you pet them. Why?
I don’t get the impression they do. They might be scared of certain Pokémon that have dangerous powers or that humans don’t know much about, but I’m trying my hardest to think of anyone who says a Pokémon is “evil” and I’m really not coming up with much (not counting phenomena like the Shadow Pokémon from Gale of Darkness and Pokémon Go, who have been transformed by an external force and can be “purified” to return them to their peaceful natural state). Individual Pokémon can certainly be evil, like the Malamar from the X and Y anime or Meowth from Team Rocket (maybe Meowth is debateable as he has several redeeming qualities, but he certainly self-identifies as “evil”), but species of Pokémon aren’t inherently evil. When Yveltal appears in the games, it’s a pawn of Lysandre, and in the Diancie movie, it’s treated as extremely dangerous but not really malevolent, more like a living natural disaster than a villain. Tyranitar and Hydreigon are much the same, destructive forces of nature more than evil beings. Mewtwo is, I think, intended to be more complex than just outright “evil”; Necrozma is destructive because it’s diminished and broken; most Dark Pokémon that are mischievous or violent are treated as being dangerous in an animalistic way.
The only ones I can come up with, the only Pokémon that I think are ever implied to be by nature actively and deliberately malicious, are a few of the Ghost Pokémon that literally represent “evil spirits” – Banette and Spiritomb and the like. And even then, the inspirations behind Spiritomb’s design imply the possibility of redemption: the 108 demons of Water Margin become heroes; the 108 temptations that lie between mortals and Nirvana can be overcome. For Spiritomb, the same has to be possible. We’re told by the Ultra Moon Pokédex that Banette’s curse can be broken by treating it with kindness. And I suspect that this should be the default assumption – that even when Pokémon are violent or destructive or malevolent in nature, there is a way in. And that way in commonly involves macarons, doughnuts and/or curry.
I think fundamentally, Pokémon are animals, and Pokémon the series takes the view that humans have a responsibility to be the enlightened stewards of the natural world. We’re supposed to show them the difference between right and wrong (or, in some cases, accept that they are beyond our understanding of right and wrong). What we’re not in a position to do – what I don’t believe the series ever endorses us in doing – is judge them.
Except for Drapion; Drapion’s a piece of $#!t