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.
The Wizard series of enemies can cast powerful magic from afar, but approaching them at close range will cause them to phase out as they teleport to another location. Not only are they invincible to everything except for spells as they do so, they can quickly regain form and blast you with a fireball, stunning you long enough to turn invisible again. An entire group of them can be a problem if you don't have a mage to dish out spells to break up their chanting and teleporting.
The goofy-looking hourglass enemies can completely freeze the entire party, and the attack that causes this only takes a full second to start up and doesn't use any MP. If you're fighting a group of them, they can repeatedly chain these attacks together, leaving you utterly helpless as they decimate your party.
Thankfully, at least in the PSX version, the freeze timer keeps going even if you open the menu, letting you recover from their attack much quicker.
The Salamanders and their palette-swap relatives. They have fearsome strength, HP to burn and their breath attacks are capable of inflicting poison, paralyze AND stone in one fell swoop. They're bad enough with a full party, let alone solo runs or coliseum fights.
Easily the worst ones of all are the Live Flayers in the Cave of Trials. They are extremely fast, come in large packs, and attack with unparalleled viciousness. There is pretty much nothing as likely to make you want to break your controller as making it almost all the way to the bottom of this long and difficult dungeon (in which you cannot save your game) only to have your level 180 characters destroyed in seconds by these nightmares, losing hours of progress and possibly several dozen levels of experience. The only chance you have is to have maxed-out Parry stats and spam Killer Moves which keep you airborne, and spend as little time on Floor 11 as you can possibly manage.
Ensemble Darkhorse: Leon. When the manga adaptation conducted its first popularity poll, Leon took 4th place (behind Ashton, Claude, and Rena), despite the fact that he hadn't even been introduced to the story yet.
Zadkiel/ Ruprecht also has some fans despite being very insignificant to the game other than being one of three bosses and one of the Wise Men to discover Filia's death.
Fridge Horror: Anybody you choose not to recruit dies... though, at least, the ones living on Expel get to come back to life.
Note what was said in the spoiler: Did you already have eight characters before Nede, eg you got Welch? Well consider this: Chisato and Noel BOTH die. only got one? Then guess what, the other one dies. If this was Noel, the last thing you said to him was "who's going to watch over the animals?"
It's actually a lot worse than it seems at first: Every living creature seen in the entire game dies, and it is only at the very end that some of those deaths are reversed. This includes your Synard. One of the last of her kind, who chose to help the party of her own volition, and who also happened to be a mommy. That last point means nothing now that the entire species is extinct.
Meanwhile, it's a pretty bittersweet affair if they live. They may be alive, but now they're both stuck as outsiders on a planet that isn't their own. There's not a whole lot of work for a journalist like Chisato on Expel and she's lost all of her friends and family, while Noel's lost all of the animals he cared for. The endings with them alone seem to imply that both are still having trouble adjusting to their new surroundings.
Did you pick Rena as your protagonist? Then guess what? Leon dies no matter what you do! And since it happened well before Expel was destroyed, it's highly unlikely that he's going to come back!
Debatable. Since Leon's solo ending includes his parents, it's entirely reasonable to assume none of them ever died, or that if they did, Expel was brought back from a time before it happened.
Game Breaker: Several exploits and facets of the game can render it very easy, especially on the lower difficulties.
The Customize skill can grant party members access to powerful weapons well before the enemies' strengths increase to balance. An noteworthy example is that Claude's ultimate weapon, Eternal Sphere / Aeterna, is customizable just over halfway through the first disc, a weapon that is only truly outclassed after completing the Bonus Dungeon.
Eternal Sphere / Aeterna is itself a Game Breaker; beyond an impressive 1600 ATK stat, granting several elemental resistences, and other stat increases, the weapon also shoots out multiple stars with each successful hit. Each star can also damage an enemy, and it is very easy to stunlock any enemy sans the Final Boss and the last boss in the Bonus Dungeon by spamming normal attacks with it.
Bloody Armor can be this; it grants invulnerability at the cost of rapidly draining the character's HP.
The "Scientific Ability" and "Kitchen Knife" skills are this in the early game, granting +10 and +20 Strength bonuses per level of the skill; at low levels, they can easily triple Claude's damage output.
Genius Bonus: It isn't that hard to tell, original English version aside, that the Wise Men are named for angels; more specifically, the ethnarchs of the nine angelic choirs (Lucifer is the obvious outlier). Not so easy to notice: Their ranking is in the reverse order of their namesakes. Metatron, ethnarch of the seraphim, is the highest ranking in Jewish lore; in the Wise Men, he's one of the three least of them, along with Jophiel and Zaphkiel (themselves named for the cherubim ethnarch and thrones ethnarch, the second highest and third highest). Meanwhile, Gabriel is the leader of the Wise Men, not to mention the vessel of their creators' soul. But according to angelology, he's the lowest-ranking of the ethnarchs, heading the...um...angels (contrast to archangels, principalities, etc.). This is important because the lower-ranking ethnarchs are considered to be the ones closer to humanity, the higher-ranking ones closer to the divine. In other words, Nede was implicitly appropriating divinity, and all the impunity typically associated with it, themselves with the creation of the Wise Men as galactic enforcers.
Hilarious in Hindsight: at one point, Claude mentions having a dog at home named Roddick. What makes it even funnier is that you realize who named it, making Ho Yay in the previous game.
Ho Yay: Ashton in both a Private Action with Claude and his ending with Noel.
Ironically, that Private Action also unlocks one of the bigger Ship Tease scenes between Claude and Rena.
Noel also is a victim of this, especially in some of the Private Actions in Lotus-Eater Machine Expel.
Mondegreen: A surprising number of people will swear on their parents' graves that Claude's PS1 battle cry for Ripper Blast is "pear into peaches" rather than "tear into pieces."
Player Punch: The death of Ronyx. Not only does this send the protagonist into a rage at Indalecio, but Ronyx was a pivotal and well-liked player character from the first game.
Expel getting destroyed. Sure, it gets better, but holy crap...
Nede sacrificing themselves to save Expel. Consider that Nede's a little closer to home.
So Bad, It's Good: The voice acting in the PSX version of the game is just so terrible at times, namely Claude, that it's actually humorous. The PSP remake has completely redone voice acting which, for good or ill, is much more competent.
Notably, this game has been held up, along with Resident Evil, as a prime example of how not to do video-game voiceovers.
That One Boss: There is a boss battle where you fight this pair of Egyptian apes called "Harfainx" ("Halfynx" in the PSP remake) who have 50% parry rates, know exactly when to counter-attack to push your characters back, and - in the half-second gap while you're running back towards them - can drop a spell that takes off half your hit points. Later in the game, when you're searching for the local Unobtanium, they show up as random encounters. ...As 90% of the random encounters. ...In packs of three.
Haniel and Michael. They're able to chain cast spells to the point where you can't do a thing and have your party dead. Oh yes, did we mention that they love firing multi-hit attacks when you're trying to deny the other one from casting?
Seriously...How would you feel knowing you were adopted, and that your real parents died like...Hundreds of millions of years ago?
Claude gets to see his father's ship getting blown to pieces by the ten wise men. With his father in that ship.
Philia is an even bigger one. What with her dad being the Big Bad and all.
Noel and Chisato will die if you don't recruit them. You can rest easily knowing that the people from Expel you didn't recruit (including Welch) are revived at the end of the game...but not either of them.
Woolseyism: In the original PS1 version, the names of the ten wise men were changed from the archangel-references and given much more original sounding names like Indalecio. The 2009 remake is obviously way better, but this was one of those things that some people actually do like better about the PS1 version.