I think the key difference is that WRPGs give the protagonist control, more control over story outcomes, more control over how they look, more control over what kind of fighting force they become. In JRPGs, the protagonist is an individual with their own lives, their own skills, and they grow into who they are, not who you necessarily want them to be.

Like in Tales, the JRPG i'm currently slogging through. Lloyd is a fighter who wields two swords with a degree of technical prowess, aside from choosing whether he learns S type techniques or T type techniques, i have no control over what he's going to grow into, he's going to grow into a stronger swordsman. I can't make him an archer or a mage or whatever.

WRPGs usually tell their story in dialog. JRPGs tell their stories in long drawn out CGI cutscenes.

They both use cutscenes, WRPG give you choices in them though.

In WRPGs, cutscenes are becoming interactive and playable. Here is how Mass Effect 2 executes cutscenes:

Mass Effect 2 Gameplay Footage

Pay attention to the intercut between the gameplay, dialogue and cutscenes.  Notice how the diagloue is part of the gameplay, and how the gameplay is integrated into the cutscenes.

So, in terms of execution of cutcenes, Mass Effect 2 is WRPGs are way ahead of JRPGs.  JRPGs still cling to the old model of "gameplay, then stop to watch cutscene, then get back to gameplay, etc."  The cutscenes are getting more and more beautiful (as well as longer and longer,) but they are static and separate from the actual gameplay.

On the other hand, WRPGs have evolved and made progresses in terms of executing cutscenes.  WRPGs are putting gameplay into cutscenes, so cutscens are actually becoming part of the interactivity and gameplay. 

Both WRPGs and JRPGs have cutscenes, but they are very different in terms of how they handle cutscenes.

WRPGs give the illusion of choice. In the end you get the same linear story 99% of the time though, with a bunch of side-quests. Maybe I just played the wrong ones, but every time I try one I get the same main story regardless of the "choices" I make plus or minus a few worthless dialogue changes. The story plays out ultimately in the exact same fashion regardless of which worthless side quests you have done. I would kill for a game that offered true choices and actually had a dynamic story.

The "illusion" of choice is better than a strictly linear gameplay with no choice.

Some WRPGs do offer some real choices.  Let's use Mass Effect as the  example again.  At one point, your main character has to sacrifice one of the two key characters: Ashley or Kaiden.  One of them has to die.  The two characters offer very different  independent plotlines -- and whoever you sacrifices will not appear in Mass Effect 2.  I think that is a very significant choice.

JRPGs often do NOT even let the players choose the main character's name, appearance, class, specializations, starting stats, diagloue and behaviors.  That's ZERO choice, absolutely no choices or whatever.

Thank you I was about to say this

And to be perfectly honest this is why I will prefer FF13 over any WRPG this gen

KOTOR was the only one whicha amazed me by its story telling, but maybe  I was so amazed as it was actually a good star wars game, they aren't easy to find

Actually that's false. If you take The Witcher, choices you make early in the game can alter the story later on, depending on who you help, kill, fuck, or fuck over.

Dragon Age recetly does the same.

Even if there is jus an illusion it's still a big difference, since I don't have even that illusion in books. Meanwhile JRPGs offer NOTHING when compared to books when it comes to the story. Also, no video game can compete with books when it comes to storytelling, so that makes linear storylines pretty bad. Cinematic games are the WORST games in existance (MGS4 is a great example of a good game gone to shit).

*cough* Dragon Quest *cough*

Ahem, excuse me.  Don't know what came over me.

Actually Mass Effect is a terrible example. Mass Effect is an extremely linear RPG with very few choices, nowhere near the quality of the recent The Witcher or Dragon Age.