Oh I agree the anime has bad writing, but I think the Pokedex is one of the lesser evils. League flukes, Iris, etc. are fare eviler imo
As for Red I was solely basing it on the Johto challenge since it's what people always bring out. Sorta like how "player" Red has a Mewtwo but Johto Red doesn't have one. As for TR, I thought they were more dangerous in Johto since their actions reached out more, like the Red Gyarados. At most they only killed a Marowak in Kanto.
What in Kanto Team Rocket had complete control over a city.