Grandia Xtreme

Dragon Quest 1 has the most generic story, but since it was the first JRPG, then maybe it gets a pass.

Lightning Returns was a fun game with a "WTF, not sure what is going on in this story."  You can kind of say that about every Kingdom Hearts after the first one too.

Xenoblade Chronicles had the most disappointing conclusion.  I got really invested in the story and characters and then during the last 1/3 of the game, the story just became this giant turd.

Well, then you could count almost any RPG before the 90s (Ultima/Wizardry/Bard's Tale/Wasteland/Might& Magic notwithstanding), since they didn't have enough memory to implement anything resembling a coherent plot, and what plot they had mostly was just in the manual.

From everything I've heard about it Kingdom Hearts easily takes the cake.

Octopath. That's the top 8 worst plots in a JRPG.

The Last Remnant.

FF13 for being boring
Kingdom Hearts for being convoluted (it's basically cool looking scenarios tied together with some vague story to make it work, if it doesn't work, timetravel)

Kingdom Hearts for the overall plot, it was simple at first. Not played 3 yet, will later in the year so I know how stupid it's gotten.

Out of the FFs, FF13, as many have mentioned before. Overly complicated with weird words thrown at you with no explanation, characters coming in, having 2 scenes but apparently important to the plot then fighting them like they mattered... was weird.

Star Ocean 4 and 5, with 4 it was more the acting was so bad it put me off, with 5 it was just dull. 3 was good however.

Resonance of Fate - Did this have a plot? i played a fair amount of hours in the overly long dungeons and never knew what the plot was.

I played it (switch version), but I would also list FF15 as a JRPG with a bad plot. The story starts okay, but after the first half it becomes worse with every chapter. To ultimately end with a totally unsatisfying ending.

Persona 5's issues are not related to the school system. 

Persona 4 Golden is one of my favorite games ever. I played it 2 hours, put it down for 3 months because the beginning is awful, and then binge played it in 4-5 days.

I was almost dreaming about Persona 5, and it seemed like they fixed the issues of P4G so it should have been a contender for my favorite game ever. But actually, I still didn't finish it (I'm in the last part, just before the true last boss), even after 2 years. Why? Because sure, they fixed almost all the flaws of P4G.

But the story sucks. And it was the main strength of P4G. The game was flawed, sure, but the story and characters were great and made the player want to continue. That's also why they managed to do like 5 spin off of different genres with the same cast. 

But P5 story? Instead of the relaxed, friendly and kinda relatable group of friends fighting a close and personal menace in P4 (you feel like a part of the group and root for them), we got a group of stereotypical one dimensional exceptional high schoolers with no team feeling at all, unrelatable and boring, involved in a shady and far away political scandal that no one cares about. *yawn* No interest. Even the scenes were it seems like characters might seriously die, the biggest reaction I got was "Oh, well, too bad". Can't care less about them. Even the characters of P3, that I played years ago and didn't even finish (the  dungeon was a bore, and I got the ending spoiled) brought more memories and feelings.

That's why I still didn't finish P5. I play a few days, then I put it down for a random reason, and then I just don't feel the need or will to play it again, because I don't care what will happen. Even though the gameplay, the OST, the graphics, everything else is a dream come true, the story and characters are a bore. I hope they'll fix that for P6.

Otherwise? Fire Emblem Awakening. Won't write a huge block. This game is my biggest disappointment ever, bad on every aspect, and the generic and messy time travel story is no different. Still didn't play Fates because of this one (and Awakening was one of my most anticipated games too, I have to stop anticipating...).