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In Pokemon: Origins we may see a much better explanation of how Pokemon League gyms work. In the episode Red fights Brock, the latter asks him how many badges he already has, after Red makes it obvious he is a fresh rookie, Brock picks up two Pokemon out of many on set.
This means the leaders are already grand experts on the field, possibly picked from the elite of the League to represent a city of the region, so they accomodate to a suitable challenge of the people arriving to develop more and better trainers. Onix and Geodude are the ones fit for starters. You may remember in Gen II that once you arrive to Kanto and take the challenge of the gyms, all the leaders have very high leveled Pokemon on the team because you already champed the Indigo Plateau, so they do not need to hold back on you, hence why Brock has Kabutops, Omastar, and others instead.
The Pokémon games are played on the eyes of a specific trainer from a specific town, not everybody is born in Pallet Town, so maybe a rookie starting in Saffron City, for example, would be fighting against maybe one Abra and Drowzee of levels 9 and 12 respectively.
This is exactly why they are called gyms, they are designed to make better trainers from every corner of the region.
