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Any of you play a pokemon game called 'Pokemon: Uranium Version'?
In that one, the gyms are categorized by habitat. That way, the gyms still have themes, and the pokemon can vary alot.
Example: The Cave gym can use Zubat, Geodude, and so on.
Although this formula does lean heavily on all the fakemon in-game, the system could easily work in official games, now that we have over 700 pokemon.
Of course, it'll never be like that, just saiyan'.