It is true, Japanese games are lagging behind, mostly because of the obvious taboo nature. It is becoming better; Fire Emblem Fates being a more prominent example. Funnily enough, Persona 2 had the opportunity for a gay relationship, which was then rescinded in P3 and P4 (there are flashes of this with Aigis, and a very tentative exploration with Kanji).

But yeah, western games, especially western RPGs, are becoming more progressive.