And my response to this would be the same one every time a topic like this comes up. I don't need a story to reinvent the wheel to compel me. After all, there are all those theories about 3, 7, 25, whatever plots and that every story is a retelling of one of those magnificent 7. http://www.ipl.org/div/farq/plotFARQ.html
What I would LIKE to see, though, is better writing. And, like D-Rider said, more COHESIVE storytelling. Take a look at Lost Odyssey. The most compelling parts of the game were the Power Point sequences because they were written by a novelist. That game shows the dichotomy between effective writing and hackneyed writing; the difference between writing from a novelist vs. a video game scenario writer. And I bring up Grandia III again. It had the seed of a beautiful and simple story about a boy chasing his dream of flight and the subplot of a mother's struggle to rethink her "little boy" as a man grown and let him spread his wings and fly. But instead of those lovely themes being cultivated, we got a hot mess. Like drowning a beautifully cooked artisan steak in cheap, no-name ketchup.
A good storyteller can make even a simple tale seem grand. The joke would be that "the current JRPG twist of that is making the obvious seem profound."
And I have to bring up To The Moon. You can argue that it's not a JRPG and all that, but it proves that a video game story doesn't have to be all flash, epic bombast, pomp, and melodrama to effectively stir gamers' feelings. It presents a simple story that runs deep and is very compelling.
(And as always, I always quote these paragraphs from one of my editorials: http://www.rpgfan.com/news/2009/640.html
Although I've played a lot of great throwback-style JRPGs from independent developers, I would like to see them go beyond refining standard JRPG conventions. I'd like to see them also reinvent, redefine, reinterpret, rewrite, and/or just plain shatter those age-old conventions. One trait that made me love Anachronox so much was that though it played like a Japanese RPG, the storyline, character archetypes, writing, and visual style were distinctly American. In these key areas, Anachronox did not try to copy or emulate Japanese conventions, making the experience feel genuine rather than being the equivalent of that "weeaboo" kid in school who acts like an anime character in order to "become" Japanese.
I am sure there are scenario writers who love JRPGs, but are tired of JRPG character relationships never going beyond the level of superficial kindergarten crushes. I would like to see them write a script where the character relationships are more fleshed out, mature, and believable, with teenage and/or adult characters that speak and behave like believable teenagers and/or adults respectively. Maybe an artist tired of the glut of stock fantasy trappings can create a vibrant modern, contemporary, or post-modern setting; a setting not used often enough in RPGs. Maybe a composer who thinks certain genres of music are underrepresented in these kinds of games can create a soundtrack that fills those voids. The potential is endless. It goes beyond what has been done before, and if mainstream Japanese developers aren't going to realize that potential, then it's a ripe opportunity for some of these underground, non-Japanese developers to step up and put those fresh or underutilized ideas into a new breed of J-style games.