Yeah, reuniting the islands should just be a process in which a human Japanese civilization players needs to go through in order to successfully accomplish later UHV goals.
Sorry for repeating this, but I think those hostile-independent cities should
-be autorazed upon conquest so players can have more say on city placement
-if an AI-player controls Japan, these independent cities should be hard-coded to be destroyed at certain dates in order to help out the AI players who are typically bad at conquering these
If this Japanese hostile-independent civ idea works out well, I think a similar model could be slowly, in the far future, applied to
-a Moorish independent civ, to give the Spanish something pressing to do in Middle Ages
-a Scottish civ, to make Englands Middle Ages more interesting than just waiting for astronomy
-a Chinese hostile-independent civ(s) (maybe something representing real civs like the Jurchens etc
or stuffs like like Xirong, Beidi, Dongyi and Nanman. This/these civs could be like the Japanese-independents in the sense that they dont represent a particular barbarian group, but just the fact that challenges were faced by the civ they encountered)