Well with themes that DON'T involve moral virtues.
Before the first generation, team rocket was a good team that helped out others, then their leaders son disappeared, and their leader snapped making a bunch of plans to find his son, like using DNA to find him, and then in the First generation, its about Team Rocket making Mewtwo from Mew's DNA, which ultimately made scientists think "can pokemon breed?" Hence generation 2, where eggs appeared, and Team Rocket sends a massive signal across the world, turning various pokemon into shinies, with that wavelength still floating around, just not as strong. and then in the 3rd generation, 2 childhood friends who liked team rocket, and tried to figure out if by rocket,they meant the sky. So each thought of it their own way, the sun, or the rain, which seperated them into enemies who nearly destroy a region through two gems, and when a certain kid named Cyrus watches this on the news, he begins tinkering with machines and suchwhich, trying to make a peaceful world where this stuff didnt happen, however, due to him being tainted by his parents, ended up turning things for the worse.... News of these things travel around the world, where another kid, believes that any pokemon that was captured is treated badly by his trainer, and swore to release every single pokemon, and let them be their own beings. and thus the story continues...