These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Ending Fatigue: Minor in the main story, but if you want to get the Golden Ending it becomes nightmarish. To get the Golden Ending, you have to do plot related sidequests, of course. To unlock some of those sidequests you have to have done another sidequest to obtain some items which lets you get some items needed to, you guessed it, get another sidequest. Some of these, if not all, are Guide Dang It, take forever to do, or are just plain annoying. It really makes you want to just get on with it.
Evil Is Sexy: Queen Protea has quite the figure in her official art.
If the comments of some fangirls both in Granorg itself and on the Internet, Dias apparently counts thanks to his "dreamy eyes".
Fridge Horror: Eruca probably spends most of the game thinking she screwed something up when she brought Ernst back and the fact that he doesn't remember her is her fault. Making matters worse, she's not in the party when they learn the real reason, so at best she finds out after he disappears and spends several months thinking he's dead, and at worst she never finds out at all and he actually is dead.
Game Breaker: They require another party member to use a movement skill in order to be truly effective, but Aht's traps are among the most damaging abilities you have at your disposal since it will critically injure if not one-shot anything that lands on it. Taking the time and effort to unlock her most powerful trap abilities will completely trivialize most fights since they'll be doing the kind of damage you wouldn't normally see unless you had an extremely high combo score.
Goddamn Bats: The monsters in the sewer that look like tiny pigs made of jelly. They tend to leap out of nowhere and take you by surprise, and they can drain your health and MP.
The Japanese fanbase was quick to note some similarities in the motivations of Heiss, the Big Bad and one Akemi Homura. There is an unsettling amount of fanart of the former in the latter's outfit.
Moral Event Horizon: When Queen Protea orders the city set ablaze in the second chapter of the Standard History, regardless of whoever gets caught in the inferno. They even allow their soldiers to kill Princess Eruca, her own (step)daughter.
Likewise, General Hugo in the Alternate History, who abuses his position as the mouth of the Prophet Noah so as to fulfill their fantasy of ruling the entire continent by using everyone beneath them as mere tools, sending them to their deaths while double-dealing with Selvan and Dias under the table to build a power base under the pretext of war. They even deliberately set Stocke and Rosch up to march to their deaths by leaking details of their missions so as to kill off potential threats to their plotting, and deliberately lied to the whole of Alistel long after the Prophet Noah died by putting false words into a dummy, so as to manipulate the entire country into doing whatever he pleased.
Nightmare Fuel: Imagine marching to war when all of a sudden, you feel sick and drained. The last thing you feel as your vision fails is a grainy sensation as you crumble into sand.
Quite a few of the bad endings are horrifying. Notable examples are Marco suddenly going insane, slaughtering the entire party except for Stocke, and then giving Stock an absolutely chillingHannibal Lecture about how its all his fault his girlfriend is dead before leaving him to die, and Aht going into full Yandere mode and trapping Stocke forever in a nightmarish dreamworld where they can spend eternity together.
It isn't apparent until right near the end of the game, but Princess Eruca is going through some serious emotional torture for 90% of the story. Her brother, whose death she blames herself for, is back... and doesn't know who he is, doesn't remember her, and, initially, doesn't even trust her. Just looking at him brings up both tons of traumatic memories and boatloads of guilt, because he also doesn't know she might have to kill him again to stop the world from ending.
Stocke himself spends the entire game watching every single person he cares about die over and over, and that's only the start of a list of problems that bottoms out somewhere around the fact that he's probably going to have to give up his soul to prevent the end of the world, and his increasingly psychotic uncle would rather kill or imprison him than let that happen.
To be fair, his normal response to her is more down to earth. (With Stocke clearly melting like butter doing so...) The final proper end to the sidequest is that while he does harbor feelings for her, and ready to start a relationship, all they did is talk about it a little.
Any and all boss fights where you have to fight a giant spider. They have high attack power and love spamming the hell out of their area of effect ability. They also take up the entire battle grid, which renders movement abilities and Aht's traps completely useless.
That damn Thaumachine. By itself it's not so much of a pain, but with the continually respawning Clockwork Thunder bombs...
The final dungeon. It's a long, straight path with lots of unavoidable, immobile, constantly respawning enemies (and you're missing the one party member who would be best at taking them out), no dialogue, and not enough save points, followed by a Boss Rush.
What an Idiot: Hugo. Noah's dead and Hugo's been lying about the things he said. After people eventually get suspicious and demand to see Noah, Hugo, instead of, say, getting a guy to dress and act like Noah, just brings out a wooden dummy, which falls down as soon as someone touches it.
Not that he had much of a choice. Absolutely no-one except Hugo himself and foreign conspirators actually knew Noah was dead, since everyone but Hugo was so devoted to the man word would have inevitably spread. Apart from being too proud for such things and at the opposite end of the continent, Dias and Selvan were all set up to throw Hugo under the bus rather than assist in such a charade.