Youâre missing the point.
People donât consider Yamato had fought Jomon. In other words, people donât think that Yamato and Jomon are groups from the same era. Even, people donât even think that we know of any battles that took place during the Jomon period. Theyâre thought like a prehistoric culture, so itâs weird to have a civilization named after them in the game, just like you wouldnât want a Neanderthal civilization, right?
The Yayoi are considered to be contemporaries of the late Jomon, and they formed the Yamato later on (regardless of proportion). And then, the Emishi are considered to be contemporaries of Yamato, possibly another descendants of the Jomon, and clearly the Yamato and the Emishi had been at war. Thatâs it.
The Yamato Kingship is from the 4th to the 7th century, which is actually more suitable for the early period of AoE2 than AoE1, so the Japanese of AoE2 actually includes Yamato in its entirety. The reason we had Yamato in AoE1 was really just because we knew so little about Japan from 1000 BC to 3nd century AD. If I were designing that AoE1 civ, I would have Wa (a decent representation of Japan from the 1st to the 3rd century, including Wa kingdoms and Yamatai Kingom) instead of Yamato.
If you want Jomon and another Japanese civ for Chronicles, it should be Yayoi, or Wa, but the Jomon civ is still weird.
If you want Yamato and another Japanese civ for Chronicles, it should be Emishi.
If you want another Japanese civ for AoE2, it can be Emishi or Ainu.
A decent approach would be to introduce the Emishi in AoE2 so they could be used in Chronicles when Yamato was introduced in Chronicles. More likely that we will not have a complete Emishi civ, at best having editor units to serve scenarios.
By the way, Chronicles is not necessarily limited to the AoE1 timeline. I personally would prefer that they focus on the various clans during the Sengoku period.