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How's this for a low stakes stand-in for an evil team?
>group of anthropologists with the same goal of making people happy, but with varying ideals on how to make that goal a reality
>fairy specialist: a hippy shaman who gives his patients Morelull caps or Togekiss feathers to chew on, but the effects wear off rather quickly so his patients are constantly coming back
>ghost specialist: a youth pastor who wants to give his patients a new lease on life by dedication to a higher power; develops a sort of god complex and begins to think all of society needs his guidance
>dark specialist: runs a low-pay employment agency "look, if you feel as though your existence is meaningless anyway, why don't you at least let someone else make use of your existence in the form of free labor"; his patients are all ex-cons and people who believe being reduced to a beast of burden is the only way to repent for their crimes
>psychic specialist: a hypnotist who just bluntly hypnotizes his patients into being happy, and sees cognizance as just a burden that you can give or take away from people to make their lives easier or more difficult
>none of them are inherently malicious nor do they try to take advantage of their patients; they mistake any dissent as lies and slander from snake oil salesmen who'd rather wring money from desperate and depressed people than fix everything with the snap of their fingers
>every few towns you'd run into a couple of guys trying to peddle one of the doctors' wares. Eventually you'd battle the doctor proper, they'd realize you're not one of (((them))) and let you go on your way
>the hypnotist could be the "final boss" of the team, who has the entire town under his control
No awakening a planet busting legendary, no universe resetting, just a small beat of antagonism between gyms to keep things interesting