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Each Gym should have a unique appearance in the overworld, field music and battle music.
I agree that ideally, gyms should be set up to actually coach the player by introducing competitive elements. You could have status, items, EVs and so on. This would be a plus for players like me, who want some semblance of a challenge with the "bosses" and it would be a win for the games themselves, as this would allow younger or less experienced players to learn essential information to enjoy online play, possibly boosting the online playerbase.
Even with this, they would still keep their type specialization, because it is ultimately a game targeted at children and it would allow those who may not have a full grasp of the mechanics to still progress.
Bit of a tangent, but I'd also like whatever region comes next to have better desgin. Alola is okay, but Galar is just beyond shit.