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This is just pure idea guy-ing, and I don't think all of the relevant information has been mined from the recent leak yet either, but if anyone's interested in making a hack based on it at some point, here's how Johto looked back in 98 or so.
Some interesting tidbits:
>route 29 was a mountain route that ran through a series of caves
>Cherrygrove was far larger with temples and a gym
>there was a small fishing town with a gym before Union Cave
>Ilex Forest didn't exist yet, nor did Ruins of Alph, National Park or many of the dungeons
>Cianwood wasn't made yet, the Secretpotion pharmacy was in Ecruteak instead
>Lugia didn't exist, and neither did the Whirl Islands
>the legendary dogs weren't roaming yet, and Entei was in the Burned Tower
>far more temples and towers scattered across Johto, the other legendary dogs most likely living in some of them
>Lake of Rage was called Biwa Valley and had a temple, most likely being where Suicune lived (a later build had a gym here too)
>Mt. Silver was directly accessible from Johto
>Route 26/27 were part of Johto