Physics? We could have The legends based on the four fundamental Forces: Gravity, Electromagnetism, Weak and Strong Nuclear forces. There would be five String-theory based 'cute' legends and one Big Arceus-style M-Theory Pokemon.

Could be called Pokemon Boson and Pokemon Quark. The third game would be Pokemon Lepton!

Or the games could be called something cool like Pokemon: Species Z and Pokemon: Zero Phenotype

(sounds like a TCG deck if you ask me)