I do not want to get into a flame war, but. You said "Japan would probably be best represented as the Tokugawa shogunate in sengoku jidai. selecting the 3 most powerful clans of the era. including Ashikaga and two other powerful daimyos "
Which has 3 problems that I had already laid out,
1. Tokugawa Shogunate is founded after the sengoku-jidai, this was just a sort of grammatical error on your part, I assume, you mean the Tokugawa clan during the sengoku? Sengoku period is from 1467–1573, although some people say it continues until the battle of Sekigahara in 1603 with the establishment of the Tokugawa Shogunate.
2. If Japan was modeled like the Tokugawa Shogunate, then all of the daimyo's land would already be under his direct control, if you want it to be modeled like the Sengoku-jidai, then a lot of cities belonging to "Japan" would be strange.
3. Ashikaga were not a real power after the Onin-war, and were just used as fake "kings of Japan" when the Tsushima government wanted to trade with Korea. Also during the Sengoku-jidai, the Ashikaga, would be the Shogunate, not daimyo...
I said that since Oda Nobunaga was the ruler of Japan, in the game, then it should be a representation of all Japanese history. If you want to base Japan on the Sengoku-jidai, then Oda would probably be the city state, since the Oda, and its successor, Toyotomi Hideyoshi, unified Japan, (which ended the Sengoku-jidai).
I don't understand any of your points, I am sorry. I am not trying to be rude.
I was being ironic, about the US states being the US's city states, since they are a part of the US. In the same way that, Daimyo's provinces were apart of Japan during the Tokugawa Shogunate. Although Texas would be good, in someways, California (Republic) and even Hawaii (the Kingdom of) would be good city states for the US, it would not make sense, to me, if Dallas, or Los Angles were apart of the US civ, and they were allied with the city states of Texas, California etc. In the same way, having the Shimazu as a city state, and having Satsuma, or Kagoshima as cities for Japan.
I think Japan should be represented as Japanese history, from Yayoi to now. i.e, the rivalry/tributary/colonies, of the Yamato, the Tokugawa Shogunate, and the Japanese Empire. And not focus on a mix of The Edo and Sengoku periods, which would add to confusion with Japanese city names and city states, also because they are all purely, ethnically, culturally Japanese. Were as the other choices were/aren't and would make more sense if they are not under the direct control of the Japanese civ