Is Johto The Forgotten Region?

Gold/Silver were released at a time when the whole franchise was still trying to figure out how a sequel to the incredibly successful R/G/B is supposed to look like.

Gold/Silver were known in development as Pocket Monsters 2. Kanto was expanded by Johto, and so was the number of Pokemon. Johto thus existed as a mere appendage to Kanto. It's purpose was to expand on it. It's therefore more logical to instead look at these two regions as a single big one. The Kanto Pokemon are native to Johto just as much as Johto Pokemon. Thus, the type of Pokemon Johto Gym Leaders use can be explained as them pulling from a common Kanto-Johto source.

"Generations" as a concept didn't exist yet. Nobody could imagine a different villainous group than Team Rocket. There was no "National Pokedex". Most of these features were only introduced in Hoenn. It was actually a huge surprise (and a controversy!) when Ruby and Sapphire dropped the player into an entirely new region that was not connected to Kanto.

Today, you (and many others) look at Johto not having its own league as a bad thing. But back when Ruby/Sapphire were released, people were shocked to learn that the Indigo League is not "the" league. That there are other leagues in other Regions. The Pokemon franchise found its footing in what came to be known as Gen 3. And Gen 2 started to look like an awkward experiment that GameFreak didn't wanted to repeat for future sequels. Can you imagine an alternate history, where the Indigo League remained the premier League, where Hoenn Gym Leaders mostly use Kanto-Johto Pokemon, where most Hoenn pokemon are locked to late game areas, where Team Rocket is always the main villain, where after beating all Gyms you travel to Johto and Kanto? Back then, a lot of people were really angry that this isn't what happened when they first played Ruby/Sapphire.