I'm sort of mixed on the state of JRPGs. I think my biggest problem comes from what has happened to Japanese storytelling since the mid-90s. It's almost like stories have become unnecessarily complex and overstuffed with Philosophy and Psychology. To me, part of that "unnecessary complexity" is the excessive use of proper nouns. It may seem like a strange complaint, but when you bring up so many terms at once, I feel like I need a glossary just to play the game. (Eventually, I get used to them, but it does take a little bit of time.) To be fair, it isn't so bad if the names are fairly normal, but when you get to games like Final Fantasy XIII with "l'Cie" and "fal'Cie", and my brow is cocked in a way that would make The Rock proud. I've been playing Final Fantasy XIV lately, and while it's technically an MMO, the game does force you to go through all story quests if you want to proceed to newer content. Some of the names are fairly simple like Garlean Empire, but then you get the names of the people from said empire such as Gaius van Baelsar, Nero tol Scaeva, and Rhitahtyn sas Arvina. (Keep in mind that those midle terms such as "van" and "tol" have a meaning too.)
My issues with the JRPG stories aren't usually limited to just JRPGs or even games. In watching anime, I tend to notice the same sort of problem where the story seems fairly normal, but all of a sudden, it takes this wild and crazy turn. It makes me wonder if there's this sort of obsession with originality in Japanese story writing? I think my problem with that is that originality isn't nearly as necessary as some make it out to be. Tropes often get a bad rap, but what makes a trope bad is if the writer just lazily implements it. An interesting example of how a fairly basic concept can turn into something fun is the manga/anime One Punch Man. The show probably looks a lot like a standard, shounen anime ("shounen" is Japanese for "boy" and refers to anime aimed at about 10-16), and arguably, it is one. What's interesting about it is that while the show features your typical overpowered protagonist, it knows how to do it in a way that's still interesting to the viewer. Another problem that I have with the weird twists is that they often seem a bit slapdash. A twist can be an incredibly powerful narrative tool, but a proper twist is usually written by including clues throughout that subtlely point toward it... or at least enough to make the reader/viewer say "hm?". The movie Sixth Sense is a good example of this as there are details that clue the viewer in on it. (A good example is how Bruce Willis's clothes never change throughout the movie.)
Outside of story, I can't say that I'm too fond of some of the mechanics. Honestly, I prefer turn-based combat in my JRPGs. There are games that I try to play over the years that focus on action combat, which is usually some weird mix of turn-based and action. An example is Ni no Kuni, and unfortunately, I gave up on the game because I just couldn't stand the combat. I was in some boss battle, and an AOE required me to swap over to another character just to tell them to defend. The whole action just felt so cumbersome, and that combos with another complaint that's in a similar vein. When you get an action-y combat system, the games typically use an AI to control the other characters. Let's be real... these AIs are bad. I mentioned Final Fantasy XIV above, and I'm constantly fighting against companion/summon AI in that game. There's a quest type in the game that requires you to pacify weakened creatures, and my Chocobo companion and any summon will continue to attack regardless of its state. When you pacify the creature, it goes neutral and stands in place, but can still be attacked. If you attack it enough, it drops out of pacify and attacks again... and you also lose credit for it. So, whenever I do these quests, I just put my Chocobo in Healer Stance and refuse to let him attack until I'm done. Fortunately, pets have a direct "attack" command, but without it, they'll still go back to the pacified mob. You also have to do duties (instanced quests) with NPCs that act as a role... usually healer. Sometimes, getting them to heal you feels like a lesson in futility. Long story short, based upon this, I prefer system that give me complete control over my entire party.