The one thing that ruins (for lack of a better word) many good JRPGs for me is a bad script.
One JRPG recently made me go into an utter nerd rage. I really enjoyed the game (gameplay, story, characters, everything) up until one point where whoever was writing the script just plain hit a wall.
Spoiler:
In Star Ocean: The Last Hope International, when Edge decides to give his technology to the human researcher and ends up blowing up the planet. That entire scene was so badly written I actually got angry. It was bad enough that he went completely emo afterwards, but good god how can I take a game seriously when that kind of bullshit happens? it was completely redonculous. Been awhile since a game has done this to me.
End Spoiler
It is one thing when the script is meant to be zany, wacky, or whatever, but there are to many times JRPGs want to be taken seriously, then just completely go off the deep-end and cannot be taken seriously.
