A lot of things are wrong with JRPGs today.
#1 - They are hardly ever turn based. And yes, I know that this is a matter of opinion. I just vastly prefer turn based jrpgs to "action" RPGs. Western developers, especially Bioware, are so far ahead of the curve in terms of action RPGs that the Japanese attempts fall flat for me.
#2 - Graphics, although I guess that isn't really a new issue. When consoles moved to CDs, graphics became a huge selling point, not just for RPGs but for consoles as a whole. It had a particular effect on the RPG market, though. RPG developers started spending a large amount of their dev time and budgets on sweeping, visually impressive cinematics in order to capture the graphics-hungry new consumers. Unfortunately, it came at the expense of gameplay and especially story writing. When characters were sprites, they had to be extremely compelling for a gamer to really relate to the story. Now, though, you can just have a party of spiky-haired androgynous white people, give them big swords, and sprinkle the game with cutscenes of them swinging said swords, and it's a lot easier way to get a game out. They are trying to sell games on visual appeal instead of actual meaningful content. As technology has improved, this has become more and more pronounced.
#3 - Enix :P