Wouldn't that require everyone else to start over and for the levels of the Pokemon in Johto to be adjusted? If the levels aren't adjusted, then after beating the elite four in Kanto you end up facing gym leaders in Johto with Pokemon that are 40 levels below yours. If they are adjusted, people in the process of completing Johto are suddenly significantly lower than all the Pokemon around them and by the time they get to Kanto, they'll be significantly higher than all the other trainers and wild Pokemon around them.
It would require a adjustment to the trainer scripts depending on which region u have completed first.
Wild pokémon levels don't get adjusted.
The problem is that since there is a lvl cap of 100 for pokémon at one point all the trainer battles will be somewhat the same.
The only real solution would have to be that u should start over and get to choose a new starter pokémon and are forced to leave the rest of your pokémon behind in their respective region and are not allowed to access the pokémon box from that region at least not until you beat the elite 4 of the region.
There is no other solution honestly since if u would allow players to bring in pokémon from the other region u could probably face roll every trainer up till the elite 4.
Even if lets say u needed to have a certain badge before pokémon up to lvl ?? will listen to u it will be the same.
I pretty much re-played trough pokémon blue at one point again with 1 lvl 100 charizard by trading back and forth between blue and gold and despite him not listening most of the time that 1 time he does listen he pretty much 1 shot everything.
So it all comes down to one of these options
- Allow pokémon from another region but rely on the badges of that region to determine if they will listen.
- Start over completely with a new starter pokémon leave old pokémon behind in the other region.
- Or scale all the trainers up to have pokémons of lvl 80 - 100 resulting in even more redundant battles.
Keep in mind that these options are for if the existing Johto were to be adjusted.
Re-creating Johto with new events and scripts is a whole other thing (Even then it needs some sort of comprimise).