The Ainu are at a severe geographic disadvantage (climate and the like), so it's almost impossible to make it so they match the population and economy of Japan or become the dominant culture in the Japanese archipelago. Even if things go really well for them, they'll likely be subordinate to the Japanese and/or Russians for at least some of their history.
But I can definitely see an independent Ainu state in Hokkaido emerging. You still need a somewhat pre-modern POD, since the island hasn't been majority Ainu since the Meiji era colonization. And they might have to gain their independence from Japan after an occupation era, like with Korea.
Also, when thinking about this question, it's probably most useful to think primarily in terms of culture rather than ethnicity.