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.
Disappointing Last Level: The end game feels very rushed, with the player blowing through the Ten Wise Men in groups at a time.
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.
Ashton is also so supremely popular that many forget that he's an optional character.
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.
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, which is easily solved by including Opera or Noel in the party to spam Healing Star or Fairy Light, ideally while equipped with a Fairy Ring and a Ring of Mental Power so they can't run out of MP.
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.
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."
Narm: Nall briefing the heroes on the Ten Wise Men. We see the Wise Men brutally massacre people in monochrome shots. These scenes would be actually gruesome if it weren't for the deformity of the figures while the Wise Men are realistically proportioned.
Narm Charm: The characters' dialogue during battle sequences (such as Chisato's exaggerated "Oh no!" upon seeing a group of enemies) can come off as this, due to their (to modern audiences) weak audio quality. Some fans even complained because the voice acting was fixed for the Second Evolution remake.
Even the voice acting in the remake isn't perfect. There's just something incredibly hilarious about Claude shouting an overblown, "Dammit!" if he fails at item creation.
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.
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?
Ugly Cute: Rena certainly has this opinion of Creepy and Weepy once they shrink down and graft themselves to Ashton's back.
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.
Even worse that Ronyx believed his own son was dead, and never lived to find out that Claude was alive. If you're playing from Claude's POV, the flashbacks in the Fields detailing their relationship don't help at all, as you realize they can never resolve their issues now.
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.