Note: It is only my personal opinion that jRPG stories are all shitty. I'm not trying to say my opinion is a fact or anything. I simply do not hold it in high regard when someone says "This game has a good story" or "that game has a good story" because to me, if I went down a list of games that whomever said that believes had a "good story", chances are I'd disagree with pretty much all of it.
To me, the best stories in games so far are those that keep it simple, and use the inherent strengths of the interactive and visual medium to exploit what makes gaming strong.
For example, I believe Wind Waker told a fabulous story - although, the details itself were simple and there were no major plot twists, it was told in an extremely expresive fashion, allowing its strength with gameplay to benefit from its presentation (the way Link's eyes follow objects, for example).
I think games like Shadow of the Colossus, which are simple and open-ended, also tell a comparatively good story by game standards. It's pretty much avoiding the pitfall of game writing (since there seems to be no good writers in the industry), while using the visuals to provide gamers with an elegant, thought provoking theme.
Note that I'm choosing games with little in the way of epic narratives featuring 10,000 page scripts. Even if what is going on the screen is epic, the actual story details are restrained.
Games for the most part are never restrained, which is my biggest problem with jRPGs (and most Western Games too). They tend to feel gamers are retards or something. least that's the way I feel when I play these games.
I think right now, that's where gaming is at for stories. Most of them beat gamers over the head with themes and have no eye for how to appropriately utilize a medium which is both hands-on and visual.
We have games written well but which could have worked as books, because they were obviously written by talent (Planescape Torment). The gameplay itself, however, was not so hot. It's exceedingly rare when I game does both, because I don't think the industry is yet mature enough to do both. At the very least, there are very few developers which contain the talent to do both at the same time (both good gameplay and presentation/story).