I don't have enough knowlegde of Korean history to comment on Silla-Joseon issue you see, but what I can say is that China has the same issue. It's repesented with multiple leaders from different dynasties that are further away from each other than the Three Kingdoms of Korea. Only logical way to fix the issue you see, is to remove Korea and add Silla for Seondeok and Joseon for Sejong, but most civ players don't care about Silla or Joseon, they care only about Korea.They could've kept one and replaced another. Right now it just seems like Korea is stuck with head of Silla in a body of Joseon. It just doesn't feel right to play a Silla queen in a clearly nation that is Joseon.
edit: Made first sentence clearer.