>gen 1: team rocket killed cubone's mother, channelers are possessed
>gen 2: whatever the fuck was the evolution signal, cinnabar's island fate. With remakes, there's Silver's relationship with Giovanni.
>gen 3: hex girls in the japanese versions, implications of kyogre/groudon if they ever went full berserk. If we count remakes, there's also mauville corporation and its infinity energy, implication of meteor's impact scale, and Prof. Cozmo's family
>gen 4: lake trio powers (one can erase your memories, one can make you an emotionless husk and the other can do what is more or less petrification but without turning into stone), old chateau implications, Cyrus' last words in Platinum, also his fucking parents;
>gen 5: ghetsis is basically abusing N, he wants to impale you; he also lost right arm and probably right eye. the implied fate of the bridge ghost girl
>gen 6: new team is basically nazis, lysandre wants to kill major part of population; ends up killing himself or possibly giving you and him immortality; AZ's fate; the ultimate weapon
>gen 7: lusamine went nuts, lillie, gladion, guzma and possibly hau come from abusive families
I probably missed older things, but fuck, it's been easier to name this kind of stuff for each next region.