It depends on how you define "best story". Is it complexity and depth? Honest simplicity? Well crafted plot twists? Convoluted power struggles?

There are tons of different types of stories, and I enjoy many of them for many different reasons.

I love Lyndis's story in Fire Emblem, because I think it's incredibly well crafted, and has some little things that people usually miss. Such as the implication that Lundgren ordered the slaughter of the Lorca.

I enjoy the plot of Final Fantasy Tactics Advance because I think it's incredibly well written, exploring some incredibly deep points with a fairly simple setup.

I adore the plot of Golden Sun, because it is a perfect travel story. As with The Voyage of the Dawn Treader, it's a simple main plot that shines because of the numerous sub plots within it.

I relish the plot of Persona 3 for being one of the best themed works of fiction I've ever seen. It explores the psychology of how one copes with death so well, from so many different angles, all punctuated by its fantastic cast.

I delight in the plot of Bravely Default for the subversions it brings to the genre, for the simplicity of the setup, and for having one of the greatest endings to any game I've ever played (it's in the top three, it's tricky to break those down though).

I appreciate the plot of Megaman Battle Network 3 for the fantastic job it does in developing depth and maturity as the plot progresses.

I could go on, but I'm running out of verbs to use to describe how much I like the plots of these games. I like the plots of most of the RPGs I play. Which has "the best"? It depends on my mood, and what I'm looking for in a plot on that day.