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.
Anticlimax Boss: Hyperion isn't easy, but if you have protection against instant death, he's not particularly hard, either. Since he comes right after the hardest boss in the game, this makes him look like a bit of a wuss in comparison.
Also the battle themes for Felgorn (Boss3), the Omega Team and Ortas, Zawu's theme (Slow05), Lorenza's theme (Peace03), and the music of the Towers (Farewell2). Though the game's soundtrack consists of standard RTP content.
Also used in the game is standard RPG Maker 2003 content, and they all receive a quality boost due to how MIDI's work. The Omega Team, Ortas and many dungeons receive this treatment.
Demonic Spiders: Any enemy that spams nasty status effects, especially confusion.
Hilarious in Hindsight: minor, but when struck by lightning during battle, Matilda looks like the character Lightning.
It Gets Better: The story really starts to pick up after the Imperial civil war arc. It also begins to get better after the first arc, but that's where you start actually learning about the plot instead of just participating in a bunch of wars.
Castor and Ethan's "shocked" faces are extremely exaggerated. It's a toss-up whether any given player will find this suitably chilling coming from otherwise very composed characters or giggle hysterically. (Either way, though, it makes it obvious that Ethan needs a hug)
Castor's "angry" face is even weirder than his "shocked" face, and without the same Not So Stoic factor, since by the time you see it he's already had a bit of a meltdown once.
Ortas's "shocked" face too, when bemoaning the death of his love. Bonus points for it being during one of the most serious scenes in the game. Behold.◊
Sometimes the dialogue gets... just a wee bit cheesy, particularly whenever someone's having a traumatic flashback.
Nightmare Fuel: Here and there; notably, the fates of Tazar and Helio, the latter made worse by the fact that he knew exactly what he was doing and the backstory events in Cromwell. It just gets worse when you find out who that terrified teenager who stabbed Wolfram was.
That One Attack: Ugh. So many of these. Many, many bosses have devastating full-party attacks that will likely leave you in critical health, (if not totally wipe you out) and the Bonus Bosses of the four Towers use two different attacks each. Both attacks are full-party, deal a large amount of damage, and inflict a nasty status effect.
Castor's "Maelstrom" is also up there as one of the worst. It causes Chaos, Berserk, Slow, and Petrify all at once while also doing a good bit of damage, and since you have to fight him several times, you'll see it a lot.
The Marid King's probably the first that'll infuriate players... especially considering it's impossible to backtrack and the dungeon's pretty darn hard at that point.
The final showdown with the Omega Team, as not only do you have to fight all three of them at once, they've all gotten at least five times stronger then they ever were. (Yes, even Earp)
Also the Riftgate, what with it being completely unbeatable without spamming a certain spell that costs a truckload of MP. In a game where MP restoration items are extremely rare. "This won't be enough to kill you", Zawu says. Yeah right.
The Riftgate is much easier to kill once you realise it's also vulnerable to one-use attack items that deal 'normal' damage. That includes grenades that are easily obtainable by stealing from goblins. They deal almost the same amount of damage that the spell does, but are useable by anyone without any MP cost.
And Yad al-Jauza, who relentlessly spams you with extremely nasty full-party status effects and HP/MP draining attacks; better hope you've got the right status protection.
The Fire Dragon. Even with the right gear and spellcards, it's still a boss you have to beat with just two characters - not counting that you may not have your best spellcards at disposal because they were equipped by other members when the party got split.
This one is made enormously easier if you picked up the item in an earlier dungeon that makes a character absorb fire damage or traded in some Hex tiles for an Undine's Charm, which halves fire damage.
The attack that causes Chaos is also a pain. Both Hilbert and Zawu are fast enough to use Green Herbs to mitigate the damage and move before the dragon does (although Zawu will likely have low max HP compared to the team since they join at a low level), but having Chaos inflicted on a character when you only have two is super dangerous. Zawu comes with a White Gown (immune to Chaos), but Hilbert can easily get confused and kill Zawu off if he's not protected, and you'll likely have a Talisman equipped since you've encountered the really nasty Petrify and Instant Death attacks already.
The Final Bosswill rip you to shreds the first time you fight him unless you've collected all the cool swag from the bonus dungeons. If you finished any of the hardest ones, though, he'll be ridiculously underlevelled and can be soundly beaten.
That One Level: The moving platforms in Archaeopolis are infuriatingly slow, and their movements aren't synchronized, which means it often takes several tries just to get them to line up correctly. Fortunately, the dungeon itself is fairly short.
That One Sidequest: The Black Mausoleum takes a long time just to unlock it, and even then, make sure you have the Invisibility Ring or Dark-element absorption gear or be prepared to be destroyed by the extremely powerful monsters there. Also, the Gate to Elysium, while not having any random encounters, has four extremely powerful bosses. The first three aren't so bad, but the final one has a whopping 200,000 HP and extremely powerful attacks, one of which hits twice and can deal over 10000 damage per hit. The reward is well worth it, though.