Interesting thread, but there are quite some things I disagree with. Let me start of by saying that I used to play quite some JRPGs in the past. I have played them up until the PS2 generation (starting from the SNES one, as the NES period was one where I could only play every now and then) so I do know what I am talking about.
First of all, let me cut to the most major issue I have with JRPGs; they are repetitive. I have to admit that I like action based games better, but that is not my major gripe with it. A great example is Grandia. The battle system is quite good; I remember spending a lot of time with it and having good fun. But even the Grandia engine wore thin because of one thing; I had to fight the same enemies over and over again. Eventually, battles became a routine and not a challenge.
It is not Grandia alone that makes itself guilty of it. Tales of Symphonia, Tales of Symphonia 2, Final Fantasy, Xenosaga, Shin Megami Tensei, Wild Arms, Kingdom Hearts are games that all come to mind. All these games are games that turn boring by the time I reached the 50% mark. Not because their system is inherently bad, but because the games throw everything they have to offer at you during the first hour and then expect you to find that same routine fun for the remaining 20+ hours. Normally, I tend to master these mechanics quite fast, so having to perform the same action which I have mastered over and over again becomes tedious quickly. It is not so much the problem that the game does not introduce new elements during the game, but that the core mechanic is just too limited.
Another major issue with JRPGs is the fact that for all the things they do right, they tend to screw up one or more things royally which in turn will mar the overal experience greatly. A recent example that comes to mind is Valkyria Chronicles. For a strategy game it had quite some promise; mechanics were fun albeit a bit limited in terms of units. Graphics had a nice style to them and the story was not bad (though not exceptional, but still enjoyable). It had all the makings to become a classic. That is if it weren't for the fact that the enemy AI made me think I was fighting a bunch of monkeys with guns and the game that essentially WANTED me to act like a retard and throw all tactics out of the window. Another example is Eternal Sonata. The game is pretty (although at moments way too saturated), but the story is downright bad. It had so many things it could have done greatly, but just moments after the interesting bits were introduced the characters managed to turn it all to crap. A great example of this is when at one point the characters were argueing whether there was something like good and evil with 2 warring nations and concluded that both of them had just their own ideals, which happened to clash. So far, so good. Then, just a few seconds later when someone else makes the remark "but then, what is true justice?" they can only answer with "we are not good enough to make those kinds of decisions". Eeeh, What!? Another part was when someone was dying and seriously took 5 minutes or more just to breath the last breath, this while she was going on and on about someone she started to love in the most retarded way I have ever seen. Then, when she falls down and I was glad this was over, she stands up again and rambles on for ANOTHER 3 OR SO MINUTES. The Chopin bits felt like a bad attempt at edutainment and the game felt to me like the makers had to show the world "look, we like Chopin!". On top of that, the animation is horrid. Extremely horrid. Not Bethesda horrid, but it gets a very close second place. You know they cant do animation if their idle states are the exact same pose as the leonardo pose used to rig the characters.
What also annoys me is the way they overexpose their worlds. A great example of this is Tales of Symphonia. By the end of the game, you will have experienced everything the game world has to offer. In fact, you will have experienced so much and have gotten so much knowledge, it will feel the world does not have anything left anymore. I have seen quite some good fantasies and most of them had in common that they didnt want to throw everything at you. They did what was necessary, gave you a good taste of the world but they would always leave you with a sense of mystery about the parts of the world you did not know about. A good game example I feel is Zelda, The Wind Waker (not really an RPG, but what the heck). This game successfully made you feel that you were part of a bigger world, in which everything could happen; above AND below the sea. Yet, at the same time, the tale being told was complete. That is what is missing from most JRPGs however.
My last point I will make for now is the lack of tactics. At one point, turn based systems were incorporated thanks to what I feel is a more tactical approach to combat. That, and it was easy to prototype. Surely, with systems like the NES or the SNES, you could not expect the machine to handle complex tactical situations. Hell, I would even excuse the PSX. However, even when the PS2 hit, games were still not able to do much more than "abuse elemental weakness X" or "cancel attack Y". With consoles becoming stronger, I felt that the tactical element of JRPGs had regressed into "tactics for dummies". Thanks to easy prototyping, I felt that developers had grown lazy and spent too much resources on their games looking pretty than the game actually having substance.
I would happily admit that there are quite some good JRPGs, just as there are bad JRPGs. The problem is that most JRPGs I consider to be good are also the JRPGs that at least 10 years old or more; the last ones I consider to be worthy of my top 10 are those of the PSX era or even earlier. Frankly, during the PS2 era, I found them to grow stale, as if they were out of tricks. I have beaten a handful, but mostly because I had not much games back then. When my collection grew, the amount of unbeat JRPGs grew exponentially with it. By the end of the PS2 era, I had given up on them totally, asking myself whether these people knew what they were doing.