Since defending JRPG's is old hat for me, I thought I'd shift gears a little and level some criticisms at the genre from the perspective of a fan...
The biggest flaws with JRPG's, the only criticisms I'm willing to accept at face value from "His Grand Assholeness" Yahtzee is his annoyance at the untouchable nature of the story and the fact that the basic JRPG formula hasn't changed since FF7 was released.
These are BAD things that need to be improved, an RPG SHOULD ALLOW PLAYERS TO EFFECT STORY EVENTS, and I am willing to state that as a constant. Any RPG that doesn't allow the player SOME control over story events should go back to the drawing board, this should be the new standard.
As well I have gotten very sick of the Town, Dungeon, Cutscene formula that JRPG's can't let go... SHAKE THINGS UP A LITTLE JAPAN!
Grind Must Go!
Random Encounters Must Go!
Maze Like Dungeon Design (unless that's the point I guess, like Etrian Odyssey) Must Go!
Lastly... if you're going to put in Turn Based Battles, make them GOOD. If you can't look at Chrono Trigger, FFX, Shadow Hearts: Covenant and Persona 3/4 and go... yeah, my Turn Based Combat is that engaging and interesting... then you fail! Go back to the drawing board! (I'm looking at YOU Suikoden: Tierkries!)