Gamefreak wanted it this way.
Just kidding :D
They did it like that so they could add different features to the games, instead of repeating the same feature over and over again. They wanted to take-out and add something in every different game. Also, Kurt the creator only lives in Johto, so you can't have that guy twice in two regions can you? :P
Source: I read it on some Pokemon magazine. I can't remember which one...