one reason why JRPG get shat upon is that they are story based and don't give a greate deal of freedom while WRPGs give that freedom and are more action based that story, look at Bioware's RPGs Dragon Age Origins and Mass Effect and Oblivion and compare that to Final Fantasy, Star Ocean and very far back, the Sailor Moon RPG on Super Nintendo
WRPG's (Dragon Age Origins, Mass Effect, Oblivion) make it so you have choice in the game, allowing you to choose how to look and the path you follow, in Biowares games, they let you choose where you went first in terms of story, so you could not rescue that asari but insted doing the other 2 planets then going to vermire, Dragon Age is about the same, you could clear out the Tower of Magi before learning that you needed a mage from there to help out at redcliff, in Oblivion, you have the main quest line but when you did it was up to you plus at one point you could choose weather you would kill an innocent in order to keep your cover or not and break you cover (i chose to kill Cameron's daughter first, took her staff and slaughtered the Mythic Dawnwhile make sure that argonian got out alive). the tradeoff with this is that because you have control, you make the story which means that the hidden past events are normally not told, like in Dragon Age, apart from the visions you get, how did everyone know that the Arch Fiend was a dragon, for all they know the dragon could have been a very powerful lieutenant of the darkspawn, in Mass Effect, it's never really explained why Seran allied with the Reapers or every how, at the very start, he looked part machine and in Oblivion, well, can't really say much because a lot of it's past is covered in books, WRPGs are made to have a lot of the past and lore completely unknown in order to try and create a huge world out of it, there creating more games or books in TES's case
in JRPGs (Final Fantasy, Star Ocean, Sailor Moon) you given the illusion of choice but you follow one path strait with a lot of side stuff, places are block off to you by either having some kind of blockade, over powered monster who you can't fight at your level or making locations unknown to you until you progress though the story, like in Final Fantasy, mainly XII, you can't get into Guravagin because of the Myst wall and you need to complete the 3rd chapter because by then you have the fire esper which you need to summon in order to enter, in Star Ocean, you don't get the location of another planet until the story of the planet your up to is done (or done at that point), in Sailor Moon, at the beginning you can't get to locations until the girls transform and when they split up to find those crystals, have very hard monsters who don't become easier until you build up your character to be the boss, not to mention that most places you go to are closed off so say you play as Ami (Sailor Mercury), you can get back to Tokyo (where Derian, AKA Prince Derian) until you get the crystal she's looking for and the other crystals that the other Sailor Scouts are looking for because the story is that they don't get back together until they have all the crystals and return at the same time, plus also, JRPGs have huge cutscenes in order to explain stuff like the past of an area or terms you might not know or try and patch up some holes that have been made in the story at the start of the game, they aren't really created to make a new world of future games, that's why most Final fantasy games aren't related, hell, Vagrant Story on Play Station is in fact set in early Ivalice which is where Final Fantasy XII is set where magic is considered outlawed and evil
ofcause, apart from the above technical stuff, there's also that when the localization happens with a JRPGs, since the US is normally the first to get it hands on it, the US think it knows what the rest of the western world wants and tries and change a lot of the Japanese references, best example for this Shin Megami Tensi: Persona, the original one on the Play Station, look it up on Wikipedia and you'll see what i mean, this changing costs a lot more more (which then equates to more money and time) that it would to just make a new game with their own references, so companies do this insted, plus also, you really only are able to understand JRPGs in the west if you know Japaneses Culture and most westerners don't do this for obvious reasons, it's the same reason a manga like Sengoku Yuko doesn't sell, it's because to know what a Yuko is, you need to know of Japaneses folklore to know just where the name and meaning of "Yuko" comes from (ie, why is at a Yuko is an Immortal Fox when they look human, why can't they be just an Immortal without the fox like ears)