Me trying to figure out the difference between Ryukyuan and Shinto beliefs is probably like someone over there trying to figure out the difference between Church of Christ and Baptist without speaking any European languages.
You get it with a bit of wiki reading. Shinto is the japanese state religion and Ryukyuan was the local religion representing a seperate identity with distinct practices. Incorporating it into shinto is the thing to do if you want to make them into japanese. It is like the difference between roman and celtic gods. It is part of their identity.
The exact nature of the differences are not that important. It is not like you split of because you have a different opinion about the nature of the son and the father. You are split up and so you develop different practices and beliefs.
