JRPGs are weird, not Japanese games in general. Japanese devs in general understand the philosophy behind level structure, enemy placement, game flow, pacing, what motivates the player and how to teach the player new concepts through game design better than Western devs do. See: Classic Castlevania, Megaman, or as a more recent example, the Souls games.
That being said, companies like Square who pay immense attention to their Mary Sue cardboard cutout characters and consider "character design" (and that's in terms of their visual design, not writing) to be the most important aspect in games, are terrible and misrepresent the virtuosity that does exist in Japanese game design. A lot of people say the Souls games "feel Western" or label them as WRPGs, but that's just because they don't pander to the otaku audience like Square does. The design philosophy in those games is very Japanese, and people seem to have forgotten what that means.
To put it another way, Square is a terrible company and JRPGs are terrible games. Stop playing them, or if you must play them, stop trying to analyze their stories. The devs obviously don't care about them, so you shouldn't either.