I enjoyed the stories of the Suikoden and Phantasy Star series. Phantasy Star III was just plain ugly, so it doesn't count... and Phantasy Star II was too early to have perfected the gaming.
Suikoden II is my favorite RPG of all time.
Honorable Mentions:
Phantasy Star IV
Albert Odyssey: The Legend of Eldean (or whatever it was called)
Valkyrie Profile
Final Fantasy VIII
Also, I bet Xenogears, Xenosaga, and the Lunar games would also be high ranking.
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