I know you are occupied with other things right now, but some ideas hit me, how the cloning could be showed and explained in the game.
Cloning concepts:
Mirror Hall – a hall with a mirror or multiple mirrors. If someone touches their crystal surface, their reflection comes to life and enters the PyTFall world. The clone would be just a look-a-like, with 1/3 traits reversed (big boobs = small boos, brave = coward and so on) or just 1/3 of the traits from the original. The Mirror Hall would be able only if discovered by exploration.
Crazy Scientist Lab – a crazy, lab-coat man wanting to combine science and magic to gain immortality. Constantly looking for new test subjects (give him a girl to clone, 1st time 10% of success, 2nd 10-20%, 3rd 10-30%, 4 the scientist tried to clone himself and succeed name would change to <Scientist name MK I>, cloning of a girl is now 25-50%, every next visit some increase in the % if cloning fails girls die). Also he could have a strange hobby of collecting other people hair (material to clone) so you had to pay with girls hair for the service. And if we would have different sprites the MK after the name also could change with the graphic design as another clone would be created and upgraded.
Temple/Altar of a God – I would propose a god of chaos or some kind trickery. He would make people doubles for fun or just to create mayhem. It would be a copy of the girl but with some evil traits. If the god would be a trickster it could be kid-like, MC could offer candy to the god as payment. Chaos would ask for a “little favor”, later on would send MC on some quest to do some evil things in the city if not the god would end MCs life.
Underground Doctor – somewhere in the slums, in deep underground, hidden from commoners lives Dr X (not Dr X from Action Men, just placeholder name) that experiments with human body. Trying to create perfection or resurrect his beloved, long dead wife/daughter/hamster. The background could be a doctor office or infirmary from some other game. Payment: gold.
Darks obsession with cloning, theories:
Fan of Star Wars.
Fan of Jurassic Park.
Wants to recreate one of the last scenes “My stepmother is an alien”, when hot alien chicks, come to take away one dude.
Wants to mess around with Xela.