Which Japanese RPG Had A Really Good Story?

[Kansler]

I created an account just to say Xenogears. That game blew my mind.

There are many others too, of course. Many FF games have a great atmosphere. Suikoden games are pretty epic. But to be honest, many great RPG's have only a mediocre story, like Dragon Quest VIII, the Grandia games, or FFVIII.