Anti-Grinding: Job classes can only reach level 3 naturally. Further levels must be purchased with JP, which are only handed out at story events or, late in the game, from moogles in exchange for Moogle Coins.
Arbitrary Headcount Limit: You can only have five people participate in battle. This means that all Guest Star Party Members have to bow out before you meet the next, one way or another. Once the worlds are rejoined, it means that three of the Warriors are going to have to sit out battles.
Asskicking Equals Authority: The leader of the pirates is whomever can beat the current leader in a fight. Bikke, as the toughest pirate, is the Pirate King. Beat him, however, and he'll happily call you Cap'n and follow your orders.
Big "NO!": Sol, after the party is forced to kill Vata.
"Blind Idiot" Translation: Mostly a decent localization, but it does occasionally have awkward grammar. There are also a few items that suffer from it, most notably "Kenpogi" (Kenpo Gi) and "Killer Row" (Killer Bow). This could be intentional considering how most games were translated back then.
The locations of the Eidolons save Sylph and Chocobo.
There is a short bonus dungeon located in Deist filled with encounters too strong for your level when you first arrive.
But Thou Must: At the beginning of Ninja's Tale, the player takes control as Alba. Talking to Nacht during this time will get him asking her (and the player) whether she wants to steer the ship or not. No matter what the player chooses, he won't let Alba take the helm.
Barbara exemplifies this trope. Her "armor" as a Dragoon wouldn't look too far out of place at the beach.
All the female characters' Warrior and Dragoon outfits are also an excellent example. Far more skin is exposed than is covered by armor.
Chain of Deals: Buy the snack from the shady NPC. Trade it to the kid for the ocarina. Trade the ocarina to the drunk for a gear. Trade the gear to the repairman for a pickaxe. Give the pickaxe to the guy wanting to dig a well to gain his trust.
Color-Coded Characters: Each of the Warriors has a specific color unique to them that is carried over into their costumes for each class.
Doomed Hometown: Lux gets swallowed by the dark rifts immediately after Lux's crystal is shattered. And then, when the world gets restored, Lux Castle and most of the residents of Lux are still sucked into the Void and held under the sway of Despair.
Dragon Rider: The Dragoons were this, before the Empire wiped them out. The sole remaining Dragoon still is.
Dual Boss: Hell Minion and his pet chimera, Butch.
Empty Levels: Each job has 20 levels. Generally, 1/4 to 1/2 of those levels don't provide any benefit, (although leveling up do improve certain stats for the equipped job) while Memorist has a whopping 18 empty levels, only gaining new abilities at levels 10 and 20.
Four Is Death: There are four Generals and four Divine Generals working for the Empire, each with an elemental affiliation. There are also four Weapons in Nil's arsenal.
The Four Gods: The four Weapons of Nil are patterned off of them.
Empathic Weapon: Graham, the dark knight, is actually a spirit inhabiting the sword and manipulating an empty suit of armor. The events of the chapter break his ability to control the armor, but the sword is still capable of speaking, and remains with the party, both as an ally and as a weapon to be equipped by the Dark Knight class.
The Guards Must Be Crazy: Sol, Glaive, and Diana open up a secret passage and sneak into Lux Castle literally right under the noses of the guards at the door. They don't seem to notice. Later, in the same castle, the trio waltz into the throne room and hide behind some pillars, all while the guards look right at the door.
Elgo pulls this off twice in a row. First he jumps in front of an attack that would have finished the party, taking 9999 damage. Then he somehow gets up and grabs the helm of the out-of-control airship, giving the party time to escape before finally dying in the fiery crash.
Gramps does this to protect his wife, son, and entire country. Asmodai is about to finish of the his wife and child and then move on to the Dark Warriors. To prevent it, he jumps in front of his magic attack, and then uses an attack that does 9999 damage to both of them.
Graham, in Sigurd's armor, pulls this to finish off Baugauven. It only costs him the control over Sigurd's armor.
Interspecies Romance: Between Eduardo, a human, and his mermaid girlfriend. Or at least, that's what it seems. They're actually mother and son, and they know it.
Jerkass: Vata or that's what Sol thinks about him.
Job System: The series' bread and butter as usual, returning as a core game mechanic after Final Fantasy V, with some having more flavor to make up for the smaller pool compared to other games. Eight jobs are available to both groups with each group having another five exclusive to them.
Meaningful Name: Most of the playable characters have meaningful names, with most being a reference to light or darkness:
The leader of the Warriors of Light is named Sol, that is, Sun; similarly, the leader of the Warriors of Darkness is named Nacht, which is German for Night.
Dusk and Diana pull double duty. Dusk is part of day reflecting his status as a Light Warrior, but gradually becomes night, reflecting his history with Nacht. Diana references the moon, a symbol of night reflecting her status as a Dark Warrior, but it also reflects the sun's light, symbolizing her history with Sol.
"Aigis" means benevolent protection. The character starts with the Cover ability, which causes him to jump in front of characters with low hit points and take the hit for him. He is also the hero of Lux, and implied to protect the area from threats.
Vata is an alternative spelling of Vayu, the Hindu deity of winds.
Asmodai is a powerful demon in Christian demonology. In the Ars Goetia, which has been drawn upon for Final Fantasy mythos before, he is described as a king of demons who punishes adulterers. Asmodai of the Earth disguises himself as King Feyr and could be seen as punishing the lecherous real King Feyr by blinding him, aging him, and erasing his memories.
The eternally unlucky Biggs and Wedge make a reappearance as soldiers from Lux.
The village of Deist is the home of the Dragoons and their dragons.
The former captain of the Dragoons was named Abel. Kainand Abel, geddit? There's also Highwind Tower which belonged to the Dragoons and Dragons.
Gramps tries to introduce himself as "Clou-", to which Alba replies that if that's his name, her name is "Aeri-". This may double as a nod to the Spell My Name with an S translations of Aeris/th.
The King of the Pirates is named Bikke. You have to beat the pirate Mooks and Bikke in order to use the port and his ship.
There is a dungeon that is too small for you to enter, so you have to use a negative status effect on yourself to make you smaller and keep it in effect for the whole dungeon - just like some dungeons in Final Fantasy III.
In order to get to the Underwater Palace, the home of the mermaids, you need to rescue the Fairy in a Bottle held by a traveling gypsy salesman, just like in Final Fantasy I.
One of the dwarves mentions that there isn't anyone named Mr. Pyntie-hat in the village, and another says there might be something to this "rally-ho" business.
The castle of Falgabard is located deep in the mountains and is difficult to access without an airship. It was home to at least one Dark Knight. In Final Fantasy III, Falgabard was only accessible by airship and was the home of the Dark Knights.
The town of Lufenia where everyone speaks garbled nonsense. Retrieving the Stone Tablet from the Rosetta Tower (or, in other words, the Rosetta Stone) to Dr. Unne will allow the party to understand them, just like in Final Fantasy I.
The job system is very similar to that of Final Fantasy V: Jobs are learned by collecting the broken shards of the Crystal, the characters' appearances change in battle to reflect the job, but revert to normal when unconscious. Abilities are learned by gaining AP in battle for the job, and the abilities can be carried over to other jobs.
As in Final Fantasy II, the Empire has eliminated the Dragoons to all but a few men, and are planning on killing off the Dragons as well.
Just like in Final Fantasy V, the flying dragons (which look a lot like Hiryu) can be healed by feeding them Dragon Grass. Walking on the grass is harmful to humans, but it's expressed in game as hurting the party, rather than poisoning them, this time around.
Much like in Final Fantasy IV: The After Years, when the party encounters save points in the final dungeon for the first time, there are small character developing cutscenes while the party camps there for the night.
Nice Hat: The Ranger and Red Mage jobs come with them standard. Gramps, being a Ranger, has one at all times.
Nice Job Breaking It, Hero: Nacht tells the bartender the Desert Moon password thinking that he's their contact at the tavern. It turns out he was an Imperial spy and he uses that knowledge to destroy Desert Moon.
The Night That Never Ends: It's always night in the World of Darkness. Interestingly, the inverse is not true of the World of Light.
Poor Communication Kills: It's unfortunate that this version of the crystals can't talk and explain why the world is in trouble, unlike elsewhere in the series. Though not for lack of trying by the Lux Party, which was explicitly sent to try communicating with them. If it had explained that Elgo - who the Lux party was already suspicious of - was evil, they might have been able to derail his plans from the start. Instead it tries to commit suicide by guardian and sunders the world itself in panic, incidentally distracting the Light Warriors from their initial suspicions.
Also, Styx's outfit is something to look at as well.
Surprise Incest: Subverted. It seems like Eduardo is falling in love with Edna, who is later revealed as his mother. However, both of them already know about their relationship, and reveal that their love is platonic.
Took a Shortcut: Ricard and an unnamed child show up at Highwind Tower just in time. The problem? Ricard is a cripple who can't even walk without help, and the child has no combat skills. The only way to Highwind Tower is through a valley chock full of deadly monsters.