My only real complaint is random encounters, but that is being phased out of JRPGS

Having really good stuff available but out of reach till you either level up to that point to use it or find a way to access it, only to find what was a cool weapon / armor that you gained at the earliest opportunity is now weaker than the gear you collected on the way to gaining it.

Ugh, I hate that.  I mean, plot reasons making me use a particular character make sense but having to kill an enemy in a prescribed way is just annoying.  It's hamfisted and controling.  

I think towns are the most annoying part of JRPGs, though.  I loathe feeling the need to constantly talk to random NPCs because I'm afraid of missing something.

Monster Hunter is built around that idea though. 

Yeah, having to talk to every NPC, because one of them might have critical info, but 99% of them have pointless flavor dialogue. Honestly, NPCs just having one thing to say for the entire game needs to die anyway. Why can't we get Fallout 3 level text trees? That would be fun. 

Also, BUT THOU MUST! moments. 

Random battles are probably one of the most annoying issues for sure, but I would say the characters are the worst with jrpgs.

Not saying all characters are bad, but there are always those annoying comic relief characters that aren’t funny. For example, the stupid joke in xenoblade chronicles x about cooking the nopon before every freaking act starts...

Also, they always have those kid characters that have never touched a sword but can pick one up and beat a trained swordsmen 10 seconds later... a lot of their characters are nonsensical as well as a lot of plot threads.

Spending the whole game building up your party only to acquire some killer weapon or powerful spell at the end that renders all your hard work pointless.

Another annoying one is when the game asks you to "choose" something but you don't really have a choice, so it's like... why did you even ask?

Like when you tell Aeris to go home and not follow you to Sector 7, but she just goes with you anyway. So what was the point of asking me if I don't really have a choice?

I assume this is speaking of things unique to JRPGs, or annoying things that happen to be in JRPGs? I hate games with a lack of direction for example, but I almost feel like this is worse in WRPGs. 

Anyways, a few RPG complaints come to mind that may or may not be unique to JRPGs.

• Missables/Points of no return: I get that the story might force this to happen, but it's bad game design to punish you for not scanning every nook and cranny for missables before moving ahead. A good game should always give you an option to find anything you missed during the endgame at least, however they find a way to implement it. Giving up and going into a second playthrough isn't a real solution, its tedium. Which leads to me to...
  
  
• Content locked into Subsequent Playthroughs: NG+ can be a cool motivation to get me to play a game again, but knowing that I can never 100% a game without replaying through the exact same thing again just isn't fun to me. I barely have enough time for these games as it is...telling me something is locked into NG+ usually means it's content I'll never get to experience.
  
  
• Save Points: This gameplay feature needs to die in a fire. There's no reason for it to exist other than being unable to implement manual saving. It doesn't actually add any real challenge the game, it just makes it more tedious if you happen to lose after not saving for a long time. Challenge through repetition isn't challenge. It's pure tedium and nothing else.
  
  
• Lack of direction: Usually when a game just sets me on my own and tells me to figure it out, my response is: Nah, I'd rather play something else. I don't have time to go on fan wikis or spend hours looking at every random wall just to find I needed to talk to a guy three times inside a hidden wall.

• Lack of Japanese audio: There are exceptions to this (Tales of Symphonia, Fire Emblem Echoes, Third Example), but in general English audio in Japanese games always feels forced or awkward, or just generally lacking in emotion compared to the original. I don't see a problem with including it for people who can tolerate it...but at least give me the option to listen to the original audio. 
  
  
• Tedious Combat: This goes without saying. If I'm spending 90% of the game just hitting attack to rush through battles then the game is doing something wrong. It gets old fighting the same enemies over and over again, and it's worse when the combat is slow and clunky and takes a while to get through, or just generally doesn't feel rewarding.
  
  
• Poorly Implemented Random Battles: I don't feel too strongly about this, but I vastly prefer seeing enemies on the map/overworld over just randomly triggering them to appear.
  
  
• Excessive Exposition: Another thing I can probably forgive more easily than most people, but games that repeat the same things constantly or spend way too much time explaining things tend to keep my interest less. "Show don't tell" is generally a far more effective way to tell a story than just having characters explain everything 20 times. 

That's called "But Thou Must!"

https://tvtropes.org/pmwiki/pmwiki.php/Main/ButThouMust

Needing to read the encyclopedia just to understand the story

I think encyclopedia's in RPG's are great, but when you need to read them just to understand what the heck is going on in the story something has gone terribly wrong. Good writing should not require a PhD in the game's terminology. Final Fantasy XIII is a prime example of this and it made the storytelling a catastrophe.

Naming characters or places after food items

Look, naming your character after something edible might be cute once, but it gets old quickly. If you are a writer and you lack inspiration to the point that you use food items as names then it might be time for a long break. Using food is as stupid as using a safety pin as an enemy. Magical Starsign and Hyper Dimension Neptunia are good examples of this idiocy. Speaking of Neptunia, that whole game is so annoying it probably deserves a headline of its own.

Getting way overpowered for doing a lot of side-quests, turning the main quest into easy-mode

This might be a minor issue and it is something that happens in most games, but I really wish that more games used a scalable difficulty system for the main parts. In both Xenoblade Chronicles and X all I had to do was touch the bosses and they would explode because silly me took on a few side-quests too many and my party became godlike.

Taking the quantity over quality route to increase the game's length

I personally don't need every RPG to give me over a hundred hours of playtime, and if increased length comes at the cost of less quality content then I'd much rather take a short game. Xenoblade Chronicles X really hurt my feelings when it threw the lobster quest at me, which had you search for a hundred small red lobsters across the city. These could be seen from a distance so theoretically it should have been easy to fly around with your skell and pick them all up, but because of how the area loading system works you would not see any pop-up markers for many of these lobsters turning the quest into one of the most annoying "find the nail in the haystack" quests of all time. And the game already had an insane amount of content, so why the devs didn't cut that quest is beyond me.

And in that not-so-good game Hyper Dimension Neptunia they increased the amount of levels by taking the small amount of levels they had and copy-pasting them like crazy. Sometimes the very next area you got to was a carbon-copy of the previous one. To pour salt on the wound the levels weren't even good to begin with. Seriously, when creating a two-room dungeon is accomplished by taking the first room and reversing the enter/exit points to "create" a second room it's time to stop and re-evaluate our position. It did give me a laugh though, so that's something I guess. And I know I'm ripping this game to shreds in this post but it really pissed me off that much.

Stupidly long attack animations

Yeah, it's nice with really cool special attacks that blows up planets and whatnot, but the cool-factor disappears when you have to watch these attacks again and again because no one considered the option of making long attack animations skippable.

Finding collectibles that do not want to be found

Collectibles aren't bad, except when they are hard as hell to locate. Finding certain collectibles in Xenoblade Chronicles was a pain in the behind because the world was huge and directions non-existent. In X you had an excyclopedia but unfortunately "You can find it in Primordia!" is a really, really vague hint.

Trying to find NPC's or places

Yeah, another part of Xenoblade Chronicles that was a wee bit annoying. So you met an NPC, got a quest, finished that quest and are on your way back to the NPC. But you have forgotten where you met the NPC, and the game does not give you any directions so you have to waste time searching. It gets even better when there's a day/night-cycle and the NPC change position or disappears during certain hours. Fun!

The map/journal system of Baldur's Gate II isn't standard

Baldur's Gate II had a nice map with markers for locations (and I think NPCs as well) but the best part was that you could add your own markers and add your own notes to your journal! Why every RPG doesn't do this is beyond me.