I love this question. :>
Gym design is the hardest part... let's see...
Oh! I'm thinking something that emulates The Abyss from Dark Souls.
Picture an entirely black room, with a crystal-clear, pristine glass floor. Glass sculptures rise from beneath the floor, somewhat resembling how thread appears close-up - twisted strings of rough glass - and through them a low, purple light shines through, refracting light to various specific points of the gym.
I guess the gym would be a very simple maze in structure, with the rays of purple light giving you indication of where to go, and highlighting some trainers along the way, but otherwise you're completely unable to see. For the shortcut back, I guess you could walk on the sculpture.
If you haven't guessed by now, the typing would be either Ghost or Dark... I'm gonna go for Ghost for variety.
Sableye, Froslass, Rotom, Chandelure and Aegislash.
Chandelure and Aegislash would depend on the level of the gym. ~40 would be 6th or 7th gym or so.
As such, I shall give you the TM for boring, old Shadow Ball as the only other Ghost TM is Shadow Claw, and that sucks... Also, it's traditional for Gym Leaders to use the TM they give you in battle, and my team would make much better use of Shadow Ball.
AI opponents aren't great with Aegislash, but I hope that King's Shield and Shadow Sneak would be enough to make it enough of a threat to be the final pokemon.
Everything else does what you would expect.
All in all, a fairly standard gym. Nothing too spectacular puzzle-wise, but at least it's not basic math problems.