Nonstop flights fetch more $ than one-stop flights
nonstop flights to Japan, limited competition, fill J/PE/some Y, bread and butter. (JL, NH, UA all have high J-count planes)
Onestop flights to Asia? You need to fight against $400 flights (via China, also one stop). Fill rest of Y cabin with people willing to transit in Japan instead of China, at a slightly higher premium ($500+)