There are a number of different aspects to a story as well. Very hard to rank them. You can have a very basic and average story that's told very well with great pacing (e.g Ocarina of Time) or you can have an incredibly deep and well thought out story that's a bit harder to follow (Xenogears in my opinion).
Best actual storytelling I'd have to go with Final Fantasy 10, as the threadstarter suggests. Some aspects of the story itself I found a bit contrived and incongruous: did they really need to make it so Jecht was Sin? and why was that Yu-Yevon randomly injected the story (although clearly the Mass Effect writers approved)?. But the actual main character driven narrative was handled so well. Slowly coming to the realisation, just ahead of Tidus, that Yuna was going to her death was incredibly moving. And then later on realising that Tidus would fade away. Incredibly powerful stuff.