>>28998323Watsonian answer: what other anons already said.
Doylist answer: there weren't enough bad guys in gen one and the mangaka's only option short of creating original ones was making some good game characters into evil ones. Same reason why half the gym leaders are secretly Team Rocket members in RGB and why a gym leader is the main villain in GSC. He stopped doing it from gen 3 on where there are many established villains he could use from the games themselves (and he created new ones that one time for FRLG because Kanto still doesn't have any).