I have seen those 1-stop connections having lower prices, and of course LAX/SAN are *much* cheaper than SF Bay area.
I'm most curious to know of insights as to *why* the prices are so high to Japan.
Just simply supply and demand. JL/NH have better J/Y products using a larger space of the plane, then use the cheap tickets to fill the rest of the small plane
UA fares are mostly.tied with NH (JL and AA, joint ventures), only Delta is a true competitor (along with the other one stop options). Lack of competition = high fares. (And Japanese people highly value having nonstop)
Cheap tickets needed for the connecting flights
Outside of knowing the airlines pricing model (confidential/privileged info), that's all you can get. You can also browse stats (how many people get to Japan, how many take nonstops versus connections, how many transit Japan only)
2018, Narita 2.7mm int'l passengers, 350k transiting