What parts of JRPGs really annoy you? Here's mine in no real order...

1. Easy pointless battles

Some JRPGs will make their fights so easy that you can just turn on auto-attack, and win the fight within the first turn. No strategizing required. 

2. Long attack animations

Performing a big attack shouldn't take up a 5 to 10 second animation. And if it does, then it should be your strongest attack. One that you only intend to use on a boss. 

3. A random battle every three steps

Yep. I am not a fan of this. Maybe having one every 5 to 10 steps is fine. Every three though? That's grind. 

4. Being forced to use/lose a party member, because plot raisins demand it. 

Yeah, just let me use whatever characters I want. Oh, you've been leveling up this one character forever? It would be a shame if he suddenly became unavailable for 1/3rd of the game due to plot raisins! 

5. Windy confusing dungeons, with no map HUD. 

Oh, man I really hate it when I'm in a dungeon with a thousand forks in the road. Only one of them leads to the boss, and the others lead to dead ends or treasure. Combine this with frequent fights, and you can just get lost for ages. 

6. Not knowing where to go next. 

Some older JRPGs give you almost no real direction. You have to go to a certain area to trigger a cutscene, and before you do the game is just locked down. 

I love the Etrian Odyssey series, because it skips all of this and more. There's always a point to fights, even if it's to kill enemies in a certain manner to get good item drops. Attack animations are fast, and to the point. Random battles are once every ten or so steps, which is a nice pace. Your entire party is always accessible. No plot raisins needed. A customizable HUD map on the bottom screen, so you never get lost. Where do you go next? To the next stratum of course! 

Plot raisins?

Anyhow, I vote for crappy writing that drags on way too long. Why use ten words when you can repeat yourself fifteen times instead?

It didn´t annoy me in the PS1/N64/Sega Saturn generation, since that´s when I started getting into JRPGs because of FFVII, but nowadays I don´t have patience for random battles anymore (which weighed heavily in my decision to skip Octopath).Thankfully it seems most JRPGs have gone the 'visible enemies on map' route.

Complicated and confusing combat

Turtorials

Slow pace

Story

Tropes. Especially when done shamelessly.

EDIT: Also, Anime bullshit. Those currently playing Kingdom Hearts 3 will feel the same way.

About the only thing that annoys me about JRPG's is the plot raisins thing mentioned by the OP. I am actually irritated far more by WRPGs.

1. Pointless leveling because monsters scale with you.
2. Huge maps that take forever to walk across.
3. Lack of a coherent narrative.
4. Lots of characters with no personality.
5. Uncanny valley graphics.
6. Lack of polish in general.

In the end it probably comes down to taste though. Most of the points in the OP are things I actually like. On the other hand I loathe the Elder Scrolls, but I know a lot of people love the Elder Scrolls. Really it's good that there are different kinds of games that appeal to different tastes.

Unskippable cutscenes.

Very bad save points. I hate redoing valuable progress.

Long summon animations.

Pointless areas.

As for OP I am okay with 1,3,5,6. 3 as long as there is a way to reduce or eliminate it someway in game.

https://www.youtube.com/watch?v=688z-4SWxOQ

The only thing that can really break me is long attack animations, in general really slow combat flow I hate with a passion.

I can't force myself to finish Xenosaga due to that.

Those are part of their heritage they took from early western RPG like Ultima (6) and Wizardry (3+5)

In Ultima you had to talk to people to find out what to do and where to go. Oh, and they wouldn't just spurt out the answer at random, you had to ask each one specific questions.

Early Wizardry titles were Dungeon Crawlers, and pretty difficult ones at that. Not only was there a battle at every corner, the battles were very deadly, too. Etrian Odyssey are spiritual successors to them. But those dungeons often had some tricks to their sleeves like dark tiles, spinners and random teleports to throw you off. Or more specifically, to throw your maps off, since you were expected to make maps yourself if you wanted to know where you're going. Some titles of the time even came with graph paper for you to make those maps.

While we're at it, what annoys me most of today's RPG (both western and JRPG) are the useless useful spells, like poison, criticals or debuffs. These are so ingrained nowadays that RPGs of the 80's and early 90's seem impossible to master because everybody leaves out those spells. But back in the days those were actually far from useless, and in fact more like your nukes since high damage spells (the nukes nowadays) were often avoided or totally resisted, making them much less useful as they are today.