if i designed a pokemon game i would rebuild it so that specific pokemon spawn in specific places but the game dynamically adjusts the difficulty based on when you get in a fight in a specific area, and how many other areas you've already encountered. make it feel more open world and less like you're forced through a linear path to explore the game.
i think also traversing through an area to another area you haven't visited should trigger that "encounter" criteria, so basically you have a set difficulty in an area when you first experience it. that way the game scales as you progress through, and you can backtrack your steps to go back to weaker pokemon