This seems like one of the most controversial ones, though, because Okinawa occupies a particularly useful position in the area. It's halfway between Japan proper and Taiwan, and helps to solidify the first "band" of islands around the Chinese waters. If one was at all worried about trouble with China, it would be the most logical place to have a base. Japan knows this as well, and wants to keep the US troops where they are.
I do not really have an answer to this, except to keep in mind that these are actual competing claims on the national interest, and probably should not be swept under the rug. However, due to the assorted other bases this would have implications for (including Diego Garcia in the Indian Ocean), I don't see any real accounting for this happening any time in the near future.