I've been thinking about the differences between WRPGs and JRPGs a lot lately and I think the real thing that defines the difference is that JRPGs lean more heavily on abstraction. Whereas WRPGs historically try to simulate as much as possible.
WRPGs came from D&D which wanted to simulate as much of an adventure as possible. Of course, as a game certain elements have to be abstracted. Think of levelling, it is a simulation of personal growth over an extended period of time on a quest. Experience points are an abstraction to facilitate that growth. Whereas JRPGs needed to abstract more of those same systems and ideas due to their more limited tools. Early ass computers and all. Think of how FF1 translates D&D almost exactly, but sacrifices many of the simulated elements so that it can have the scale it wants compared to one of it's own inspirations, Wizardry. Plus, this means JRPGs are abstracting mechanics from something that already has to abstract elements.
In fact Ultima Underworld was supposed to be "dungeon simulations" and Daggerfall a "fantasy simulation" and I think why WRPGs mix really smoothly into other genres, something like the Deus Ex series.
Other example: abstractions like "random battles" are in both genres, but the way that JRPGs used them leads them to a more deliberate segmentation between story and battle which allows for story to be separate deal that can be focused on independently. While WRPGs use things like a charisma score as a mechanic that influences world interaction, which is how they tell their stories. And at this point they are tied to their genre conventions and inspirations.
I haven't put together research or anything, but these are my current thoughts on the subject. Make sense to anyone? Sorry if it's too rambly.
On what makes an RPG an RPG? I dunno... feeling, I guess.