Idea: Choose your Generation
This thread https://pokemongo.gamepress.gg/q-a/randomize-pokemon-everyone about individualized spawns actually gave me an idea.
What if when you opened the Pokemon Go App the first screen after login was "Choose your region. Johto(2) or XXXX (whatever 1 is called)"
Then when the servers generate a pokemon it generates a Gen1 and Gen2 version depending on which your client was playing.
But catching the Gen2 random pokemon if you logged out and back into Gen1 would be a blank space. There would be nothing there because you already caught a pokemon at that spot.
One worry I have with Gen2 is Dilution. It's going to be harder and harder to get the pokemon you want and or candy you want as the Pokedex expands.
If say you still havent got a Machamp in Gen1, your odds will be lower as soon as Gen2 comes out and increases the pool of possible spawns.
Answers
And if you are playing in a different region all the Pokestops and Gyms are shuffled. What was once a Gym is now just a stop. New Gyms at what were just stops. Imagine having different Gyms to hold or take down depending on which region you chose. Coins for every Gym held regardless of region and only able to chose a region every 24 hours.
There are not enough new pokemon being added in Gen2 to need something different since there are vastly increased spawn points since the game first began. If anything, the new pokemon rates will probably be similar to rates at the beginning.
Storywise this is okay because (spoiler alert?) in the Gen2 Gold/Silver games, Kanto and Johto were connected. After you finish the game in Johto, you can explore and collect pokemon in Kanto and fight and collect eight more badges.
Next year(?) when Gen3 roll out is looming, maybe something different will need to be done.