This is the distinction between antagonist and villain. Though even villains can have noble sentiments or goals that don't oblige them to be hostile dicks.
I think you've got it backwards. Heroic characters will, by definition, be disinclined to work with the blatantly evil psychopaths than they are people who were just antagonists in general in their source material. I wasn't talking about making characters that will be antagonists in this game as well.
@KoL Hey, i wanted to ask if i could have Sanaki potentially run into Meteora, since PKMN told me to send the purple-haired loli to NY. Any thoughts on how you'd like to do that (since the other guy left Meteora high and dry)?