I think you are still vastly overstating the difference in the genre's source material.

D&D, as well as many table top games, pretty much make up the core combat of both genre's. In terms of story, they aren't really built specifically to be one or the other in terms of game play. Many table top games can very easily go the route of what you would expect in a JRPG, a linear story set up by the DM the players are following along. (Hell, this is the very core of how pre-made adventure paths have always worked.)

And having complicated and deep stories isn't something exclusive to JRPG's over WRPG's, so attributing that to Graphic Novles is pretty silly. While not as much in it's infancy due to system constraints, when you get to games like Ultima IV and V there are some very deep and immerse stories go on in those games with some pretty heavy themes.

The differences in writing styles seem more explained by the kinds of teams working on them.

Specifically, Richard Garriot specifically went in with the intent to make games without any kind of writing backround.

Sakaguchi, over at square on the other hand, was a professional writer when he was brought in. Well, Sakaguchi wasn't the writer, but that's kind of beside the point.

Also, when he was no longer a part time employee, they took inspiration form the success of not their previous works (None of which were all that big), but success of Enix's Dragon Quest, a game which itself has no real roots in Visual Novels at all, but with the Wizardry games. Mind you, DQ is pretty much the prototype for the JRPG genre.

The tighter focus on a story seems to have a lot more to do with Their premise of having the writers, programers and artists working more closely together then the Visual novels they made.

Really both styles of RPG's routes are pretty much identical in nature.

The difference was Square's Philosophy at the time to involve the different parts so much, which led to the stories being more focused.

Compare that to the western developers, a lot of which didn't really make use of professional writers in the way Japanese developers did (HEll, Richard Garriottes first game published was made only by himself).