Okay I was going to post in this thread the other day and decided not to. Against my better judgment I'll step into the fray. For years my favorite genre was JRPG. Lately I've preferred many of the WRPG's.
As a fan of both genres, I think it's safe to say that "what's better" is best determined on a game by game basis. Certainly The Fallout 3 is MUCH better than The Last Remnant for instance so I don't think it's fair to say that "JRPG's are better than WRPG's" or vice versa.
This generation has seen an explosion in really good high quality WRPG's which is why I've sort of migrated away from the JRPG genre and for the current gen I'd say that WRPG's are superior in both number and average game quality.
The problem with WRPG's:
1. They can be a bit overwhelming when you first start one.
2. Because of the limitless freedom you're given, they're bug ridden.
3. If not done correctly, the combat becomes very boring.
The problems with JRPG's:
1. The story's of many of these games are almost identical and completely cliche.
2. Voice acting is almost never done right and is almost always horrible (in English) and they almost always have some stupid 7 year old girl that talks like she's 3. Maybe this is popular in Japan but most American's find it annoying. I'm sorry, I don't want to take a small girl with me into a dungeon full of zombies and guys summoning 12 headed hydras that cause asteroids to fall onto the battlefield.
3. The final bosses are

ing retarded. I don't need to fight the same dude a million times in different forms until he finally says something stupid like, "NOW YOU SEE MY TRUE NATURE!", oh really, you've been some kind of giant building monster this whole time and no one knew? Why exactly didn't you just stomp all over the planet years ago? No one could have stopped you. Also, why not just jump straight to that final fight?
4. Many have random battles which is fine but after decades of these games I have a low tolerance for dungeons that have super high numbers of random encounters where you have one every third step almost (I'm looking at you Lost Odyssey).
As far as my favorite JRPG's this generation (rated from best to worst of the one's I've played):
1. Tales of Vesperia (best JRPG since the SNES)
2. Lost Odyssey (too many random encounters - awesome story)
3. Blue Dragon (annoying children but sold traditional JRPG)
4. Final Fantasy 13-2 (stupid at times but fun)
5. Final Fantasy 13 (Doesn't quite live up to the name Final Fantasy)
6. Enchanted Arms (note, many people hate this for the shallow reason that there is a gay character in it.)
7. Magna Carta 2 (starts out shit but turns into something great)
8. Infinite Undiscovery (I ended up enjoying this more than expected by the end)
9. Eternal Sonata (has a pompous anime style ending sans the "Congratulations")
10. Phantasy Star Universe (story mode is an advertisement to pay them to play)
11. Star Ocean 4 (I've never seen a game with such a predictable cliched storyline, annoyingly long and dumb dungeons such as space ships that are 90% corridor and 10% usable space (what engineer would design such a thing?), this has terrible acting, You spend too long on individual worlds, and the final dungeon is a pain)
12. The Last Remnant (This game is pure ass. The story is so copy/pasted from other games that you can almost quote the words before they say them. When they actually say the words, they voice acting is so bad it makes characters in Star Wars episodes 1-3 look like Patrick Stewart. This game has really dumb dungeons that you go to repeatidly for side quests but oh wait, they opened a new passage that was somehow not there last time you visited! Finally, this game game has what must be the absolute worst system for upgrading characters I've ever seen. The system involves so much luck that some of your guys end up having shit weapons even though you have some truly great things that they COULD be using.)
***Notes***
I could have included Costume Quest in here due to it's direct influence by the genre and if I were to include it, I would put it above Final Fantasy 13-2.
I have not yet played Valkryia Chronicles -waiting on it to be $10.
I own but have not yet played Tales of Graces F.
I own but have no yet played Xenoblade.
I plan on getting The Last Story when it's $20 or less.
Ni No Kuni is coming out soon and I expect that will rank high.
As far as my favorite WRPG's this generation (rated from best to worst of the one's I've played):
1. Skyrim (do I really need to explain it?)
2. Dragon Age Origins (this is simply fantastic)
3. Fallout 3 (this thing grips you from birth...)
4. Mass Effect (great game though I'm not sure I would call parts 2 and 3 a WRPG)
5. Fable (Good story, good fun, annoying gargoyles)
6. Oblivion (old but damn good none-the-less)
7. Dragon Age 2 (This is half the game it should have been but it's still decent and cheap to buy.)
8. Deus Ex: Human Revolution (I debated putting this one on here since it's so different from the more traditional RPG's but it's worth a play through for almost anyone and a throw back to the original in so many great ways I had to include it).
9. Fable 2 (subpar but worth a single play through)
10. Borderlands (didn't play multiplayer so didn't think it was anything special)
11.Two Worlds (this is REALLY bad but the low budget it was made under gives it a unique quality. It doesn't take itself seriously at all. The devs basically said, "Yeah we know this game is shit so lets just roll with it".)
12.Kingdom Under Fire: Circle of Doom (this was so bad I couldn't finish it and that's saying something)
***Note***
Bastion probably could have been included, if it were in the list I would have it above Mass Effect
I own but have no played Fallout New Vegas.
I own but have no played The Witcher 2.
I own but have no played Risen.
I own but have no played Risen 2.
I own but have no played Lord of the Rings: The War in the North.
I plan on getting Kingdoms of Amalur : Reckoning.
I might get Divinity 2.
Final thoughts, I've played A LOT of RPG's this generation and this generation has been bloated with WRPG's. While there are a significant number of JRPG's I haven't played, many of them are SRPG's which I have no interest in (though I am going to give Valkryia Chronicles the benefit of the doubt). If you look at the top two games on the lists, Skyrim and Tales of Vesperia, Skyrim is superior in MANY ways but ToV's advantages are the story which is focused yet not completely linear and the acting which is absolutely the best this generation for any JRPG's. The protagonist in Tales of Vesperia a

ing bad-ass who participates in vigilante justice and essentially murders people who he thinks deserves it (it's part of the story, not a player directed activity). So as a fan of both genre, I'd say they're roughly equal though it's much more difficult for JRPG developers to make a top tier game without at least some of the problems so common in them (Bad voice acting, over the top cliches, annoying emo protagonists, too many random encounters). I think people (including myself) generally give a pass to many of the bugs we experience in open world WRPG's because we know it's almost impossible for them to make contingencies for everything a person can do. That said, if there are too many issues the game will suffer and would not be at all playable.
http://www.youtube.com/watch?v=oyFQVZ2h0V8