The only logical explanation here is that the Joys and Jennys are either Terminators or similarly lab-created clones, because “identical cousins” isn’t a thing. And since an Officer Jenny hasn’t strangled Pikachu with her ultra-robot hands, that just leaves one option.
So how was Fuji able to clone the Joys, Jennys, and Pokemon, but not his daughter? Well, cloning is an artificial, unnatural process, and Pokemon have proven to be much easier to clone than humans because they are completely unnatural clone monsters to begin with. It’s why Mewtwo survived while “Ambertwo” bit the dust like a punk.
Pokemon don’t have “babies” like normal creatures. Two Pokemon (even two absurdly different species) can mate with each other to make an egg. But the baby in the egg isn’t really a combination of the “parents,” but an exact duplicate of all the others in its species.
Since he was never able to clone humans, but was eventually able to bungle his way through Pokemon cloning, we can deduce that Dr. Fuji must have created the humanoid Joys and Jennys in the lab from scratch using modified Pokemon DNA. And he likely got the DNA from Blissey (the evolution of Nurse Joy’s Medical Assistant Chansey), who can take not only human form, but Nurse Joy form. So when you see a Nurse Joy standing next to a Pokemon, what you’re actually seeing is two Pokemon.