I heard some fan theory that Dark type specialists are generally mistrusted by the general population, so they tend to get brought into the Elite Four so they don't have to worry about local sentiments and other tough trainers can keep an eye on them. Hence, we have 0 Dark gyms despite every other type except Fairy having at least 2. The trio of Dark type members of the Elite Four and Pokemon League makes sense when you realize that the most common Elite Four types are Dark, Psychic, and Ghost. These three Spooky Scary types combined have 5 gyms and 9 Elite Four positions.
As for what I'd like from a Dark gym, I'm thinking about a possible throwback to Koga's ninja theming. Yes, ninja are often associated with the Poison type in-universe, but it seems like a good choice for Dark as well. Ninja would be the ones to make sure every damaging move had a secondary function.
The Gym puzzle could also refer to a few existing examples. Ecruteak's Ghost gym in Gen 2 uses invisible pathways, Dewford's Fighting gym in Gen 3 uses a decent darkness-based puzzle, and Hearthrome's Ghost gym in Platinum mixes flashlights in darkness with a maze. Something like this with a vertical component, and maybe some hidden ninja trainers, would be great.
ThE Gym Leader themself would use a Geninja at some point. Because obvious connections still need to be made. Besides that, Leaders usually have three to four Pokemon maximum. Some decent Ninja-esque candidates could include Zoroark, Weavile, Bisharp, and Shiftry. That would leave a big weakness to Fighting types, but that's par for the course. His signature Move/TM could be Hone Claws, Thief, Payback, or Snarl.
