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I have always thought about this! Heres what i think. That you must be a tough and experienced trainer that you are allowed to become a gymleader. Or either you ask to have a gym and have to prove your streangth.
I think to me they become as an unofficial gym first and become well known with your talents, or there could be a huge competition of the best trainers and the Top trainer becomes a gym leader and runs the city they wish.
We know how. Start your own "unofficial" Gym and hope the creepy Nurse Joy in an undercover trenchcoat comes to your Gym for inspection and makes it "official."
There have been a lot of "unofficial" Gyms in the show, like the one in "Just Add Water."