I'm not tremendously familiar with Lithuania, most of my exposure was in TW:Kingdoms or wiki, so if you could expand on what you mean by that? Just the general history of their conversion? Also what do you mean by Bhutan or Nepal? A small state that could very well be just another province of their bigger neighbor but managed to survive?
It was a small, tribal zone caught between expanding powers on all sides. Poland and Russia were reasserting themselves after the Mongols, gradually becoming serious powers again, while Germans and Scandinavians appeared from the opposite direction, settlers and semi-genocidal crusaders. It was in terms of technology, economy, and geography quite simply disadvantaged. In that sense it's position was comparable to that of the Irish.
Yet Lithuania managed to expand to conquer roughly a third of contemporary Russia and by quickly marrying into union with the Kingdom of Poland
kept that control for centuries. Naturally, that union left the much smaller and poorer Lithuania at a critical disadvantage (hence the nobility all ending up essentially Polish), but it was still a tremendous accomplishment.
For our purposes, a unified Ainu state would be unlikely to remain unified for long unless it engaged in a political alliance/union with a Japanese entity in the north. Having entered into such a union, however, would give the Japanese statelet a level of status it could never have on its own. Where without it would be merely one kingdom among dozens, poorer than most, with the Ainu connection it has practical strength and an ideological justification for independence from the rest of Japan. If the relationship becomes traditional and accepted, even conquest of the Japanese half by the southern Japanese would be temporary because the OTL logistic issues would preclude extending the same level of control to Ainu lands.
Essentially we're talking about Scotland. The country is mostly northern Englishmen, but its existence and much of its identity is derived from the Highlands. The far north fails to share either a language or economy with the south, and is dependent on it, but still Scotland survived the whole of the Middle Ages because the two were successfully convinced that they shared a national identity.
I'd argue that the Ainu could,
with a dominant Japanese partner, play the role of Japan's Scotland. Genetically and linguistically it would improve their position above that of OTL, but at the end of the day they're still hanging out in the equivalent to the Highlands and Orkney.
