You would have to ask gamefreak for the real response but I can give a theory:
Gamefreak usally makes gyms (minus Brocks gym in red/blue) have a nearby Pokemon that is weak to the gyms type. In order to keep you trying new Pokemon and changing your team to counter a particular threat. The thing about the dark type are its weaknesses. (Bug, fighting, fairy) usally bug types are the common types to find at the start of a game, there weak, evolve quickly and become nothing but a nucience for your team late game. Gamefreak wouldn't want to put bug types in an early game enviroment with a dark gym as chances are you would sweep it, but putting it in the middle of late game would cause you to have to level grind those lvl 5s from the start of the game. And grinding is boring, gamefreak wants you to keep playing their game. Fighting types are too OP for an early game enviroment, learning moves like wake up slap and strong normal type moves, mid game they are perfect against a dark gym but also take out alot of types and to keep you changing Pokemon they would move it to late game. It's perfectly viable for a dark gym late game but at that point there's only one gym + elite 4. So it problebly just got assigned that. Fairy is a reletivly new type, not really offensive (minus mawile) and the only other being a legendary. They just don't have enough for a region and to give a variety when facing a gym.
Also in most regions you have the option of a part fighting type starter, gamefreaks probably doesn't want new players doing solo runs. It defies the purpose of the game. Catch em all.
Hope I was able to understand! Xddd
