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>Simply replace any Kanto Pokemon without Johto evolutions with their Johtonian equivalents.
>Less Rattata, more Sentret. Less Geodude, more Shuckle. Less Gastly, more Misdreavus.
>Then have trainer and gym levels scale to badge count like the Wild Area in SWSH.
That's it. It isn't rocket science. The biggest reason why Johto doesn't stand isn't content or identity, anyway. Johto flies by because the level curve and Pokemon distribution makes the game devoid of challenge barring some major spikes. Giving the game a proper level curve would introduce challenge and pad the experience out without being too grating. This is the same reason why Kanto doesn't stand on its own in HGSS either despite being mostly restored. It's not fun to just steamroll through everything like you can in Gen 7 and 8.