Honestly, I struggle to find many well written stories coming from Japanese games. Western devs excel at production value, that's for sure, but western games tell much more intelligent stories on average as well. Where they absolutely fail most of the time is in blending the story with the gameplay, not that Japanese devs are any better, but western devs are pretty universally bad with that.
I dunno. I honestly don't think there are many japanese devs aside from Nintendo that are any better in the gameplay department than western devs. Platinum... Some of Capcom's studios... Some of Konami... Eh.