Anti-Climax Boss: Lost Babil in the PSP is actually quite easy to defeat, especially if, like you would expect of a Bonus Boss, you wait until the post-game to fight him when your party is at a high level with the best equipment in the game.
Big-Lipped Alligator Moment: The final dungeon is full of Crystals, both light and dark, far more than the eight taken from the Blue Planet. Interacting with each Crystal spawns a boss. The first few are the elemental Archfiends, then we get other Final Fantasy IV bosses, and then other Final Fantasy bosses in general. Many of them are completely out of place in Final Fantasy IV's setting, the Phantom Train being most prominent. Shinryu, Omega and Deathgaze can also be found in manners similar to their original games—Deathgaze and Omega are just wandering around and Shinryu lurks inside a chest. There is absolutely no reason given for why the bosses from the original game were revived, no explanation about anything at all for any of the new bosses, and no word on how they are connected to the Crystals.
Lampshaded by the party to a degree. After each fight your party members each get a single line of dialogue, often expressing surprise at the type of foe they just faced and wondering why and how their enemies revived their old foes. This is particularly amusing when you face Ultros, where their reactions are pretty much "Uh, what just happened?" They're really at a loss for words.
Breather Boss: After fighting your way through a maze full of Demonic Spiders, including Degraded Bosses and if you don't know the right path, up to 3 battles in a row with no chance to heal between them, Rydia's Challenge Dungeon pits you against Boss Gobby. Normally all he does is order his three minions to attack you, and their attacks are laughably weak. The only danger comes in when you attack him, as he counters randomly with one of three attacks, one of which is Firaga and does serious damage. But as long as you survive it you're fine, his other counters, Thundara and Bio, are pretty weak. Furthermore, if you did level grinding to teach Rydia Bio, he'll die in two casts. Bio, endure his counter, heal if needed, Bio, boss is dead, mop up the minions. The only snag comes in when he begins to buff and heal himself if you try to kill his minions first, which most players will try to do the first time they fight him, but otherwise he's a snap...
Complacent Gaming Syndrome: For the final chapter, a lot of players stick to the "original five" (Cecil, Rosa, Rydia, Kain, Edge), occasionally subbing out one or two members for someone like Golbez, Palom, Porom, Edward, or even Luca. Not to mention, you'll see lots of Bands.
Ending Fatigue: The final dungeon of the original Final Fantasy IV was 13 floors to the Lunar Core which was three or four floors long. The Subterrane of this game's final dungeon goes down 13 floors, pitting you against a boss every other floor or so, then leads into the Depths which are 22 floors long and contain a pack of bosses every few floors. Not helping the length of the dungeons are various small cutscenes along the way to provide closure to personal character arcs.
Luca, for being an effective Ascended Extra that's a powerful party member with a non-fanservicey design (uncommon for the series) and a humorous crush on Palom.
One of the most inexplicable examples of the series is Monk C from Yang's Tale. The fandom nicknamed the Monks Anderson, Brown, and Coleman. Coleman joins five levels higher than Anderson or Brown due to being recruited later, and he has a better weapon in the Metal Knuckles. This resulted in him becoming a Memetic Badass because he was significantly stronger than the other two Monks and could possibly match Yang and Ursula in damage output. The PSP release gives Monk C a darker portrait, seemingly distinguishing him from Monk A and Monk B in a nod to this.
Epileptic Trees: As mentioned above, the Depths of the True Moon contain Crystals that spawn other Final Fantasy bosses to fight you. As The Creator tells you that many worlds received Crystals to record and process the evolutionary paths of their inhabitants, there are some theories that thus take this as the implication those other Crystals came from other Final Fantasy worlds The Creator had visited and possibly destroyed.
Fanon: There are plenty of fanworks depicting Edge and Rydia being Cuore's parents due to the many ship tease moments between the two and Rydia raising the last surviving Maenad. The ending credits in the IOS version fuels this up.
Faux Symbolism: The main antagonist appears to come from the moon, looks like Rydia, and brainwashes the Eidolons to serve her. What does this mean for the Summoners, the Lunarians, and the Eidolons? ... not a darn thing. Interlude reveals she looks like Rydia mostly by chance, the moon she comes from is a different moon from the Red Moon of the Lunarians, and she uses the Eidolons apparently just because they're effective and convenient minions.
Goddamned Bats: Literally. Mostly because they're just resilient and fast enough to cast Bloodfeast on you 10 or so times per combat. Which does like 20 damage and puts "Sap" status on your party members. This is especially annoying in Edge's and Porom's Bonus Dungeons, the former of which is a Time Trial and the latter of which has a time limit.
It's the Same, Now It Sucks: A common complaint about the game is that it basically recycles most of the first game's content in a different order. It has the same dungeons, many of the same sprites, many of the same items and equipment, and even gameplay elements like abilities and spells. The story, meanwhile, is not only a lot of rehashing of plot points from the first game, but the other characters even notice this and lampshade it.
Nightmare Fuel: The final boss, The Creator. Whereas most final bosses in the series build up to an epic final battle that indicate just how hectic things will get, this time around you're against an entity that is practically Eldritch Abomination with steadily decreasing sanity, a horror-esque ambiance that pulls no punches, and, by the end of it all, a relentless and destructive foe repeatedly attacking and chasing after you which you seemingly cannot kill until a Heroic Sacrifice finally makes him vulnerable.
Memetic Badass: Monk C from Yang's Tale, spawned due to joining at a higher level and with better equipment than Monk A and Monk B. Is also known as "Monk Coleman" or simply "Coleman".
The Scrappy: Despite actually being a pretty decent character, you'll find few fans who like Ceodore all that much. It is understandable, though; he's a Pinball Protagonist who barely affects the plot at all, has very little personal growth when compared to returning characters and is so average that he predicatably gets overshadowed by more specialised characters who have less versatility but more raw power in a specific niche.
Sequelitis: Though the ability to change your party and the Band system greatly elevate the gameplay, the plot leaves something to be desired. Many events parallel events in the original game, something even the characters note. But if this adds to the ominous nature of the events that history is repeating itself, or makes the game seem a boring rehash of old plot elements, YMMV.
That One Boss: Make it two: The Mysterious Girl and Asura. The Mysterious Girl is in the back row behind Asura and lobs third-level magic at you while Asura uses a pattern of healing her, casting Shell on her to buff her magic defenses, and attacking you. The problem is that your two party members are Squishy Wizards, you cannot damage or incapacitate Asura in any way, you have limited MP, limited MP-restoring items, and with the girl in the back row all physical damage is halved so the only way to do respectable damage is via magic...except for Asura healing her every third turn or so and then buffing up her magic defense. And that's on top of the aforementioned attacks they both throw at you that you need to keep on top of.
Porom's Challenge Dungeon. Being a white mage, you're meant to help various NPCs by healing them, giving them items, saving them from monsters and putting wayward spirits to rest. But the monsters that are encountered are very powerful, you have a time limit of 15 minutes, and the placement of spirits, NPCs and your starting location is random. Furthermore, the spirits don't even appear unless you speak to the right NPCs. NPCs also bleed you dry asking for expensive pieces of equipment and wanting Esuna cast on them five times or more, draining Porom of 100 MP because she has to be the one to cast it, instead of the generic White Mage you also have in your party who also knows the spell. The most annoying part is that even if you help everyone, you're still not guaranteed to get a good item, and all but 1 of them can be gotten elsewhere with infinitely less frustration.
Rydia's Challenge Dungeon. The enemies inside use counterattacks like Blaster or Entice to disable a party member (keeping in mind you only have two party members total), their physical blows pack a punch, and you have no White Mage to buff or heal you, so you need to rely on Hi-Potions. Furthermore the dungeon is full of Degraded Bosses, namely Trap Doors and Demon Walls, and is a maze with many passages leading to dead ends, and if you pick the wrong rope in a room where you need to use them to advance further, you can get up to 3 difficult battles in a row with no chance to heal between them. The going is made easier with Bio, Rydia's Disk One Nuke, but she'll quickly run out of MP for it and your precious Ethers and her Osmose won't do much to prolong her longevity. There's a good reason that after every floor you find a save point—between the powerful attacks of enemies and Rydia's Bio spam being the best offense you have, if you weren't allowed to stop and rest regularly, the dungeon would be nearly impossible.
They Changed It, Now It Sucks: The iOS and PC release heavily redesigned the final dungeon. Rather than just a copy of the Lunar Subterrane, the dungeon is now a mash-up of various other maps from the two games. Further, everything from the fight with the Dark Knight to the final chambers is removed, replaced with a few different floors containing some of the items from the removed floors before you progress to the final floors of the original dungeon. This also means that the retro bosses from the other Nintendo-era games are gone, replaced with the Lunar Eidolons, palette swaps of the normal Eidolons. In essence, the entire final dungeon was one huge cut corner ostensibly to save time having to create new areas and enemy models. Fans were not amused.
They Wasted a Perfectly Good Plot: As described above under Faux Symbolism, the Mysterious Girl is presented as a Rydia-lookalike that comes from the moon and has the power to forcibly control the Eidolons. This provides numerous potential story threads for connecting the Summoners to the Lunarians and either or both to the Eidolons, after the original game provided some hints already (Bahamut on the Red Moon, Golbez seemingly fearing the Summoners and also being able to Summon). However, any connection between these ideas turned out to be, well, Faux Symbolism, and no meaningful revelations or story is built on the potential.
Harley and the Calcabrina dolls; Harley's abilities are fairly sub-optimal, the dolls both have terrible stats that can only be reasonably increased using equipment found right at the very end of the game and all three have a low number of bands, many (if not most) of which require ill-advised character builds and party combinations to put together, which leaves them at the bottom of the party ladder for pretty much all players once The Gathering comes around.
The Eblan Four get this treatment for their sub-par stats and bands that leaves them just above Harley and the Calcabrina dolls in the party ladder. While some of them do have their strengths (Izayoi having an wide array of healing skills and Tsukinowa having the highest speed stat in the game) Edge outshadows them all anyway.