I agree with Roto that both have problems. I do feel, however, that W-RPGs are going in a better direction these days. Too many J-RPGs are content with remaining the same. Dragon Quest is going to be the same game until the day I get AIDS and die.
Besides, many Western-RPGs do have very good stories. Mass Effect crafted a very cool world with a really good plot. I would say its sci-fi world stands out a lot from Star Wars and Star Trek. The characters are also so fleshed out. Bioware's games in general have really good stories. The Diablo games are pretty good gothic fantasies. I suppose the plethora of sidequests in Oblivion offer interesting miniature tales, though the main story is pretty lol.
I dunno. I've gravitated towards Western-RPGs a lot more these days. I don't know if it's because I didn't give them much chance before so it's a bit newer to me, or if J-RPGs just interest me less. I think when my interest in anime went poof so did my interest in what J-RPGs tend to offer. I'm sure it depends on the person to decide which is the bee's knees and which is not.