I think the problem rests mainly with the focus on creating cinematic experiences, as well as the conservative approach of most JRPG makers in general.
One of my personal pet-peeves of any modern JRPG is how long and dull attack animations are - before FFVII this wasn't a problem because there was no focus on making "cool" cinematics, but with the move to 3D, spellcasting animations started topping 10 seconds, which is just ridiciulous and eats up time I would rather spend playing the game. I have nothing against turn-based gameplay, but this is something I feel needs to be rectified.
I also feel there is a distinct lack of meaningful innovation within the genre. These days you get a lot of gimmicks and cutscenes, but you don't see stuff like FF VI's Opera Scene, which effectively changed the mise en scene of the game and created an opera within an opera, which in turn merged gameplay and story beautifully without resorting to minigames, a la FF VII.
Also, most games don't even use their cinematics to tell the story properly. For example: I don't care for the Tales' series artstyle, but the animation is simply atrocious. Good animation is one of the most important facets in creating believable, life-like characters, and Tales, along with most of it's ilk, has completely dropped the ball in that area. It's not enough to use motion capture during important cutscenes, you need to use it during gameplay or else it just looks like you have a bunch of dolls running around.













