IamwhoIamwhoamI

There are 2 things I can think of. 1: Make a hidden area for it. This would be like in Final Fantasy 4 with the dev team hidden in the game. 2: Replace the Game Freak area with "PokeMMO" area. This would probably require the least amount of work for games that have them, as it would be adding/changing dialog to characters instead of making a whole new area.