To date, my favorite Japanese RPG has been, and still is, Final Fantasy IX. Why? Because as far as plot and presentation, I find it's the most uniform, and well thought out.
What it comes down to is style. FFIX presents it's world through pre-rendered backgrounds and areas, as did all Final Fantasies of the PS1 era. Because of this style, the scenes were relatively static. You walk and move your character through what is essentially a painting, with "walls" coded into the game to create the illusion of surface and space. So you couldn't "move the camera" or center the view behind your character; what you see on screen is all you will get.
Developers worked around this by creating multiple backgrounds for certain areas, and automatically shifting between screens as you approached borders. This was also implemented during story-scenes, which of course, gives the scenes a much more cinematic appearance because of the "dynamic" view shifts.
Lastly, as you can see above, FFIX and plenty of other videogames employed FMV. Essentially computer generated movies/ shorts, these play during dramatic or important scenes, and are wonderfully directed and exciting.
The result is a great mix. The story scenes go from simple, one camera scenes, to shifting perspective and panning scenes, and finally the FMV, which can be as dynamic as a real movie. But the beauty of FFIX, at least for me, is that the story is not overbearing. Perhaps because its because the story is presented through text/ speech bubbles, that the dialogue never gets annoying, as it does with voiced scenes. The FMV's are always a treat to watch, and the cinematic panning and shifts can still catch me by surprise. Maybe the variety of methods the game used to tell it's story made it so easy to enjoy.
I'll need to chew on it some more....