I just think some people have too high of expectations for a story in a game. Not every single story has to be an epic masterpiece of something...
This is why I'm careful with my wording... it's not about the story, but about the quality of the writing for me... how the story is executed. A game like Tales of Symphonia for example, doesn't have a compelling story. But it didn't need to... the character interaction was fantastic much like Grandia II's, and it had extremely fun gameplay to supplement it. Aside from the last hour or so, neither game took itself too seriously.
Grandia III is a steaming pile of failure because no matter how epic the story could have been, the writing failed to keep me interested. This is where Lost Odyssey, Eternal Sonata, Final Fantasy XII, Xenosaga, and numerous other titles have all failed to deliver. If I don't care about the characters and dialogue, an RPG will not retain my interest for long.
Mass Effect and Ys: The Oath in Felghana are two of my favorite RPG titles. They stand on opposite ends of the spectrum as far as complexity goes with regard to storyline, but I enjoyed both a great deal. It's all about the execution.