>>35189751I actually thought that they had the right idea with Necrozma. It's actions are horrible, but it had a legitimate reason for acting the way it did. I guess you could debate whether or not it was truly evil, but like
>>35189764 said, you as the player likely don't want to have a raging psychopath on your Pokemon team.
If they ever do have a truly evil Pokemon without any shread of sympathetic backstory, 1) it should be a member of an explicitly multimember species (i.e. an asshole Lugia that causes storms at sea and sinks ships, which is entirely unrelated to the Lugia in Johto that you catch at the Whirlpool Islands), and 2) you don't have the option to capture and reform them, but are forced into destroying them.