Most JRPGs have crappy story yes but that isn't because the medium is flawed it's because of the writers.
The stories are, at best, not so terrible that they make you stop playing. That's all you can really hope for and that's all any of the writers seem to aim for. Sure, it's theoretically possible that a JRPG could come along with a genuinely good story, but it hasn't happened yet and I can't imagine it happening any time in the near future, which makes that point kind of moot.
As I said, setting, atmosphere, and characters are far more important than story. Even more important than gameplay, if the godawful shit many people play through is any indication.
Games are still, at their best, all about the gameplay. That's the one thing they have over movies, television, books, comics, etc.; you get to PLAY them. Nothing a game could do, story wise, couldn't be done better in any other medium.
I may be alone on this. In fact I'm quite sure that I am, but the strength of a games story or plot is second last on the list of features I look for in a game, right above its realism. I will skip terrible cut-scenes to get to good gameplay, but I will not suffer through awful gameplay to get to another cut-scene.