For a series with over 16 mainline entries and innumerable spin-offs, each Final Fantasy game finds a way to be distinct from everything else. The series is pretty loose on what actually defines a game outside of scant themes and naming conventions. One thing that ties the games together is the characters.
Those characters always find a way to be different across games, be it turning an enemy into an ally, or a joke enemy into a recurring cameo. While most of them are usually just a new rendition of the character between games, they manage to remix these characters to fit their new setting while still feeling like the same character at their core.
8 Bahamut
One thing you can expect in most Final Fantasy games is summons. They come in many different forms and names, from the cinematic actions of FF15's Astrals to the more direct control of FF10's Aeons. Though designs change across most games, and plenty of unique summons are introduced, one of the most powerful and dreaded is typically Bahamut.
Bahamut is typically seen in the games as the head of the gods. He first appeared as a summon in FF3, though has been a character since the original. Most typically, he is fought as a boss before being obtained as a summon, and he's usually up to some destructive actions. For example, in Final Fantasy 14 and 15, he's trying to destroy the world. Not the nicest guy around.
7 Ultros
Originally introduced in Final Fantasy 6, Ultros served as a recurring boss in the game, one who was relatively weak and wise-cracking but not really much of a threat. Because of that, they became a bit simpler to rip from their own game, often credited as Orthros.
In each and every entry, they have the same personality and appearance, a rude, purple tentacle monster. In the original Final Fantasy remake, he can be fought in Soul of Chaos Dungeon, in FF13-2 in the colosseum alongside Typhon, and plenty more. Most scenarios end with him getting cooked – a justified action.
6 Magus Sisters
The Magus Sisters are most well-known as an optional but incredibly powerful summon from Final Fantasy 10, though this was their only time as a summon, and actually their second appearance in the series.
Originally, the trio of sisters appeared in Final Fantasy 4 as a boss in the Tower of Zot, going by the names Sandy, Cindy, and Mindy in English. Though limited in character, they make up for it in personality, their tactics in combat reflecting their relationship. They again appear in Final Fantasy 14's Endwalker expansion as, would you believe, a boss in the Tower of Zot, though this time, they're revered as goddesses. A big step up from being the minions of others in the past.
5 Garland And Chaos
The words 'chaos' and 'darkness' get thrown around a lot in Final Fantasy, but they usually have an actual meaning behind them. In the case of Chaos, it represents the entity of, well, chaos. Featured most prominently in the original Final Fantasy as a force of evil, it was personified through Garland, the main antagonist. Both Chaos as an entity and Garland as a character have appeared across multiple games, usually in a somewhat parallel-hopping way.
Though Garland appears as an antagonistic force in FF9, this is only the same Garland thematically. Stranger of Paradise, however, has you play as the self-same Garland depicting their growth into the embodiment of Chaos. It's an adventure that twists the idea of the original story plenty and turns Garland into a deeper character while simultaneously still making him a boss. Anything to defeat Chaos.
4 Omega
It's pretty standard in Final Fantasy games for there to be a super boss of some variety. There's plenty of variety across games, from FF15's Adamantoise to FF7's weapons, though you'll usually find Omega. Unlike most other recurring characters, though, Omega is likely the same one across all games.
Not to be confused with Omega Weapon (great naming there), Omega originally appeared as an optional boss in Final Fantasy 5, traveling the Interdimensional Rift. The lore of Omega builds them up as a much more complex character. They're the same Omega across each game or at least off-shoots of the version in FF5, all with the intent of hunting down some great beast hinted to be Shinryu. Some ancient civilization almost always creates them to track Shinryu down, and they'll make sure you won't stop them in their quest.
3 Cid
Of all the Final Fantasy characters there are, both one-off and recurring, Cid is likely the most famous of them all. Each and every rendition of him is unique, and he's one of the most prolific characters in the series. Funny enough, despite how different he can be, you can always guarantee he'll be an inventor. And sometimes a bit of a bad guy.
How could this beloved inventor be evil, you ask? Well though he's not strictly an enemy you fight in FF8, he is partly responsible for the whole time compression and child soldiers thing, which isn't a great track record. But then there's his appearance in FF13, where he is directly an antagonist that frequently tries to kill you. He still has a cool airship in both cases, at least.
2 Biggs And Wedge
Outside of the already strange decision to name them after Star Wars fighter pilots, Biggs and Wedge are a beloved duo in the series. They always appear as a pair, with one usually being significantly smarter than the other, though brains only account for a bit of a personality. It might be odd to think of them as enemies then, but they've been on the losing side in some games.
From their original appearance in Final Fantasy 6, they've spread across plenty of games, though in Final Fantasy 8 find themselves in service of the Galbadian Empire. Here, they're a recurring encounter, and they're honestly kind of pathetic. At least they're the good guys in every other game.
1 Gilgamesh
Ah, Gilgamesh. From their original appearance in Final Fantasy 5, they've become one of the most notable aspects of the series and have managed to rack up the most appearances across the entire franchise. Gilgamesh, like Omega, is also the same character across games, hunting down a vast collection of weapons, most notably Excalibur.
Though a recurring boss in Final Fantasy 5, they've had many forms over the years. In FF8, they appear only to replace Odin as a silent swordsman. In FF15, they are an ancient and stoic warrior wielding spectral arms. In FF12, they are kind enough to give you a fishing rod despite earlier trying to kill you for your weapons. They've even had notable appearances in spin-off games, like actually stealing your weapons in Type-0. Having them literally always be the same guy just makes it a bit funnier too.