I have been mulling this over for the last couple of days.

Articulation has been somewhat challenging, but I think I can do this.

Johto is an underdeveloped region, not in the sense that it is poorly crafted or lacks character. In fact, it oozes character. It has this distinctly rural feel to it.

A number of routes between towns are poorly established, forcing potential encounters on travellers. The notable exceptions are around Goldenrod and the route to Olivine city, both of which are your major transportation hubs for the region.

No place puts more focus on this than the 3-way crossroad between Violet city, Ecruteak, and the national park. It is a thin, narrow, wooded path. Sure, it is used to gate players with Sudowoodo in the way, requiring you to take the long route, but there are other ways this could have been accomplished. After Sudowoodo is gone, you are still left with this surprisingly narrow connector between major locations.

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Something else that I think adds to this vibe and helps create a more believable, wider Pokemon world.

To my knowledge, Johto is the only region to date that shares a league venue with another region. This adds this sense of gravitas to the Indigo Plateau and the Elite 4 that are housed there.
These aren't regional Pokemon Masters. This is a national level venue.

It wouldn't be hard to imagine other local regions coming to the Plateau to compete.

This makes Johto more rural aesthetic more realistic in my mind. It exists in tandem with Kanto and a larger scale league than in isolation.

It does raise questions on the whole league/champion thing, but I try not to think about that.

Later generations, despite being labelled regions, give off larger "country scale" vibes. All-inclusive pockets that are only connected through dialogue and cameos, nothing physical or tangible.

I may have come away from my original point...
As I said, articulation is difficult.

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