The FR pairings seem random at first. But when you look at the character's personalities and roles within their games then the pairings start to make sense.
Krile and Relm are magically adept young girls with doting grandfathers who they really care for.
Braska and Amidatelion are summoners who sacrificed themselves to help save the world.
Kam'lanaut and Seifer are villainous knights who were betrayed by the people they were sworn to protect; particularly, their family members.
Desch and Leila are both a Guest-Star Party Member that can use thunder spells and are attacked by a sea monster at one point in their respective games.
Tidus and Ceodore have fathers who helped save the world and want to live out of their shadow.
Gabranth and Gau had mothers that passed away, have an estranged relationship with another family member, and their homes were invaded by The Empire in their respective games. In story, Gabranth also seems to have a soft spot for Gau.
Ursula and Ashe are Action Girl princesses who defend their kingdom from an invading Empire(although Cecil was brainwashed in Fabul's case).
Warrior of Light and Prishe knew each other very well from the previous Dissidia games, and Prishe was even the one who gave him a real name.
Vivi and Sazh being partnered represents how they were two of the first characters recruited to the party, and thus now go way back. On a deeper level, Vivi might represent Sazh's son, Dajh.
Dark Knight Cecil and Vivi were both weapons manipulated for war, and have abilities that require Cast from Hit Points.
Vaan and Machina both lost their brothers and this forms the crux of their motivations.
Yuna and Bartz both strive to follow the legacies of their fathers, and are well-rounded fighters thanks to their games' respective job systems.
Terra and Kuja both have immense magical power, share a role as tools for their respective villains, and are both capable of super-powered Trance forms.
Onion Knight and Warrior of Light are both nameless warriors of light, and Onion Knight looks up to the latter, especially after the Passing the Torch between them in the story for Act 3.
Squall and Noctis are both broody warriors at first glance and are talented sword wielders and leaders who wear black with responsibility thrust upon them that they have to grow into.
Balthier and Cid Highwind are both airship enthusiasts known for having a female partner. Also, Balthier is a "Mid" (his real name is Ffamran mied Bunansa), and he's paired with a Cid.
Faris and Wakka are both captains - one a pirate captain and the other a blitzball captain.
Seymour and Kadaj both have a ton of Mommy Issues.
Sabin and Eight are martial artists, and both are users of Phantom Rush; their FR ability is even named "Double Phantom Rush."
Ashe and Edge are both monarchs who lost their parents and had to ascend to the throne before they were ready for it. Both also specialize in lightning damage.
Aerith and Eiko are both mystical and lost their mothers to their enemies, and essentially raised as the Last of Their Kind.
Serah and Minwu ended up sacrificing their lives in their respective games. Both are also Seers.
Garnet teaming up with Braska is due to their shared summoning talent, and Garnet represents his daughter Yuna.
Celes and Basch are both knights. One is a traitor and one is believed to be a traitor, and both seek to redeem themselves.
Kuja and Laguna have an Odd Friendship in Opera Omnia, and both are theatric and love a good show (Laguna is even a movie star). The name of Kuja's FR is "Starlight Soiree" to signify this.
Maria and Trey are both tricky archers and Trap Masters.
Fujin is essentially a ninja, which is why she partners with Shadow. Both are terse speakers and specialize in throwing weapons - Fujin with Rings of Death and Shadow with Fuuma Shuriken.
Rydia is a human raised in the esper world and Terra is a half esper raised in the human world. Depending on the Artist, both also have green hair.
Lilisette and Penelo are both talented dancers who lost family to war. Penelo lost her brothers and Lilisette lost her father.
Yuri and Palom are both kids who love fooling around and playing pranks, and they get along well in the story.
Beatrix and Snow are both protectors; Snow is also one of the Save the Queen wielders throughout the series, like Beatrix is.
Seven and Llyud both have trouble expressing emotions, making them seem cold, but they're more emotional than they appear.
Rinoa and Yuna are both the female lead of their respective games and have special powers that drive the plot. Rinoa is a Rebellious Princess and Yuna is bound by duty.
Sherlotta and Cait Sith share a cat theme. Also, in both cases, their cat/cat-like bodies are artificial and remotely controlled (Cait Sith's by Reeve and Sherlotta's by her real body encased in crystal; she is just possessing the body of a cat).
Machina and Kain are both The Atoner who have betrayed their friends.
Aranea and Fang are both Action GirlBlood Knights and Dragoons who had ambiguous allegiance at first. Both also lead their own respective groups; Aranea is a commander in the Niflheim Army and Fang is the leader of the bandit gang Monoculus.
Cloud of Darkness and Exdeath are both Eldritch Abomination beings fixated on the Void.
Ardyn and Leon are both people who fell to darkness and a Then Let Me Be Evil mentality, mostly due to circumstances beyond their control. They interact quite a lot in the story due to this.
Hope and Eald'narche have been involved in a storyline when the latter tried to unleash Bhunivelze from inside Hope. They're also both Older Than They Look.
Strago and Kimahri are both blue mages. In a bit of a stretch, they both also devote their lives to a younger charge.
Reno and Quistis: One is a professional who is really a slacker, balancing his personal and work life; the other tries her hardest to be a professional but deals with failure and a demotion due to her personal issues causing hangups.
Mog and Krile: Krile loves moogles and can speak with them.
Iroha and Noel: As pointed out in the story, both come from a Bad Future and bond over their relationship with their respective masters.
Cor and Gilgamesh being paired up references Cor's Trials of Gilgamesh that he went through, which is a big part of the Gladio DLC.
Cid Raines and Vayne both struggle with being pawns of the gods or god-like beings and seek to rebel from that.
Llyud and Shelke are both new characters from a sequel game who had their emotions artificially drained away from them. Throughout the course of their games, they slowly get them back and learn how to bond with their newfound friends.
Enna Kros and Hope are both associated with Alexander and share their bodies with a god of light.
Sice and Paine are both edgy young women with some Goth leanings and aren't afraid to get rough.
Lunafreya and Rydia are both associated with water and Summon Magic, and lost their mothers tragically as children in an event associated with the hero.
Minwu and Kurasame are both mentor figures who sacrificed their lives in service to a war and to unleash a great power. Both also wear masks to cover parts of their faces.
Dorgann and Auron are both mentor figures, Older and Wiser warriors who help guide the legacy of those who fought after them. Both have also previously saved the world.
Jack Garland and the Emperor are both driven by a singular goal, and will do anything to attain it. They have also clashed in the Different Future DLC of Stranger of Paradise, which is demonstrated by the Emperor attacking Jack instead of assisting him.
Fusoya and Strago are both wise old mages and masters of magic.
Jessie and Maria are both rebels who enjoy explosives and know how to use them.
Neon and Celes are both skilled swordfighters, mages, and wielders of the Runic ability.
Rubicante and Leo once served one of the primary antagonists and had a Heel–Face Turn. Both were known for being a Noble Demon beforehand, and both had a direct hand in the destruction of one of the protagonists' home nations.
Kurasame and Cor are both mentor figures to the main party and act independently of them, and tend to be pretty stoic and levelheaded.
Paine and Dark Knight Cecil both had a close friend betray them and are associated with a red-themed branch of the military: the Red Wings for Cecil and Crimson Blades for Paine. Paine is also associated with the Dark Knight dressphere.
Lann and Reynn are matched up with the other Sibling Team pair of twins, Yuri and Chelinka.
Quina and Fusoya: Both are members of a reclusive and mysterious race that help the heroes.
Edgar and Jessie: Both are massive flirts who are part of a rebellion against an authoritative power, and talented machinists to boot.
Zack and Tidus: Both are heroic characters who are bundles of energy and have a bit of a hero complex.
Noctis and Zack are both heroes who inherit the honor of those who came before them and whose fighting style they mimic (Regis and Angeal, respectively), indicated by the name of the FR ability, "Inherited Heart." They both also share a sacrifice in common at the end of their respective games, and their love interests die too.
Reks and Jack (Type-0): Both are good-natured soldiers and swordsmen who form a fast bond in Reks' Lost Chapter.
Auron and Gabranth have both served as guardians to important figures in their worlds.
Rem and Rosa: Both are part of a Childhood Friend Romance and are dedicated healers. Both also fell ill during their games as a plot point.
Leo and Steiner are both knights in dedicated service to their corrupt monarch who struggled with To Be Lawful or Good.
Iris and Serah are both younger sisters to a stronger warrior who have both also used Moogles as a weapon (Serah has Mog and Iris has a doll that she uses as a Guest-Star Party Member to occasionally whack her foes with).
Bartz and Squall have had a long storyline of being comrades in Dissidia, demonstrated by the chocobo feather Bartz gives him. Also, both of them have a chocobo named Boko in their home games.
Ace and Setzer both use cards as their weapon and have abilities that rely on some level of chance.
Setzer and Barret are said by the developers to only be paired up only because of Rule of Cool, but they both have lost a close friend/rival/Foil of theirs in their backstories that significantly shaped who they are today.
Rosa and Lulu are both among the few playable characters in the series who are mothers.
Cloud and Paladin Cecil have both been plagued by inner demons over the course of their journey only to defeat them and become unwavering paragons of justice and good.
Astos and Kefka are both creations of powerful masters that have rebelled against them and brought ruin to their worlds (Kefka by unleashing the Light of Judgment, Astos by bringing back Jack's memories and helping him become Chaos).
Jihl Nabaat and Reno are both members of a secret intelligence service armed with batons and their games have them functioning as minor antagonists.
Quistis and Seven are the "older sister" characters of their groups who wield whips and try to remain cool and professional but are emotional deep down.
Penelo and Edward are practically connected at the hip as a dancer and a musician, where both compliment each other.
Lightning and Firion have shared a number of scenes together in Dissidia 012 and also have a rose motif in common (Lightning's Eidolon mark and Firion's wild rose).
Lenna and Neon are both Warriors of Light who tend to be the kindest and most self-sacrificing of their respective parties. Lenna is associated with water and Neon is associated with fire, but Lenna also has a secondary association with fire due to Phoenix and getting possessed by the serpent demon Melusine (whereas Neon becomes the serpent demon Marilith).
Sephiroth and Garland both sought to become godlike beings and also take pleasure in tormenting their arch-rivals. They're both also a Fallen Hero.
Golbez and Freya are both associated with dragon spirits. Golbez had also used Kain, a left-handed dragoon, to do his bidding in IV, and Freya excellently matches the description.
Queen and Ignis are both bespectacled warriors that hide their more emotional sides under complete professionalism and serve as the main planners of their parties.
Weiss and Caius are the main antagonists of sequel entries responsible for awakening Chaos in their universes.
Vincent and Prompto are gunslingers who carry a dark secret and are created as a result of inhuman experiments (Hojo's studies of Chaos and Verstael's Magitek trooper program).
Noel and Gladiolus are both protectors of an important figure in their worlds.
Cater and Lilisette are both haunted by the events that happened to their alternate selves, experiencing them either as bouts of déjà vu and a literal alternate version of herself, respectively.
Kelger and Jecht are both warriors from an older generation who have sacrificed themselves in order to stop the evil looming over their worlds.
Locke and Zidane are heroic thieves... ahem, "treasure hunters".
Selh'teus and Astos are both members of a lower class race (Kuluu and dark elf, respectively) meant to serve the "advanced" race in power (Zilart and Lufenians), and seemed to be antagonists at first before being revealed as unambiguously heroic and aiding the heroes.
Zidane and Sherlotta are both tailed humanoids with a mischievous personality who have been experimented upon by an elderly villain and had something metaphysical taken from them at one point.
Deuce and Selphie: Both love performing, and they are often shown to get along with each other and plan festivals together on more than one occasion. Both are also noted for being scarier than their sweet demeanors would initially let on.
Ciaran and Vaan are both initially inexperienced and unambitious young men who get involuntary involved with a cataclysmic plot. Both also have traveling and seeing the world as part of their core motivation.
Kadaj and Xande both have nihilistic tendencies and threw a Suicidal Cosmic Temper Tantrum over the state of their existence. Both also felt that they were spurned by a mentor/parental figure that drove them to their villainy.
Irvine and Reks are "older brother" figures to the protagonists who were involved in plots to assassinate an important figure in their worlds.
Laguna and Vincent used to work for the government before turning against them. Both also have a romance subplot that plays out in flashbacks that ends badly.
Arciela is an intelligent and taciturn princess who hides her true preference for sweets, while Quina is a talkative and simple-minded royal chef who is quite open about their taste for frogs.
Ignis and King are both the most analytical members of their groups, capable of keeping a cooler head than their comrades and coordinate them.
Snow and Rubicante are both challenge seekers who possess personalities contrasting their elements, with Rubicante being cool and collected despite wielding fire and Snow being hot-blooded and rowdy while his eidolon is an ice-elemental. They are both also the targets of revenge for the death of another character's family member: with Hope wanting to kill Snow for the death of his mother and Edge wanting to kill Rubicante for the deaths of his parents and destruction of Eblan.
Cissnei and Fujin both wield shuriken-type weapons, work for an antagonistic force and possess a sense of professionalism that separates them from the more lax attitude of their colleagues.
Yda and Sabin are both monks (although in disguise, for Yda). Both have an action-first mentality and both have access to Fire-themed abilities in their respective home games. Both are also tied closely to their siblings.
Cait Sith and Mog are both in charge of another moogle (or several, in Mog's case).
Leonora and Arciela are both demure masters of white and black magic who become protagonists of the main story of their series's continuation. Both are also involved in the leadership of their respective home cities, Leonora as one of the Epopts of Troia and Arciela as the Grand Chancellor of Adoulin.
Relm and Kelger have an interaction in the latter's Lost Chapter where she draws a portrait of him. Relm also has a special connection with Shadow's dog, Interceptor, and Kelger is a werewolf.
Amarant and Sice are both the most aloof members of their parties, preferring fighting to talking, and neither of them like to follow the rules.
Keiss and Desch are confident partners to the protagonists.
Ultimecia and the Cloud of Darkness both want to reduce the existence to nothing: Ultimecia to prolong her own life and the Cloud to fulfill its role as the bringer of Void. They also manipulated another magic user (Edea and Xande) and had several interactions in Dissidia Final Fantasy NT.
Gilgamesh and the Onion Knight are both accomplished weaponmasters that wear red.
Gladiolus and Rude are both taciturn members of an elite unit who are assigned as bodyguards to an important person.
Rufus and Balthier are both ambitious sons of famous inventors.
Paladin Cecil and Lightning are both elite warriors of their governments that decided to rebel upon learning about the truth behind their assignments and have at some point become holy warriors (Cecil as a Paladin and Lightning as Etro's Knight and later the Savior). Both of them have also given up parts of their past identity (Cecil as his Dark Knight and Lightning as "Clair") which even manifested as an Enemy Without (Cecil's mirror self and Lumina for Lightning).
Leon and Golbez are both elder brothers of one of the main heroes (Maria and Cecil, respectively) who wield the power of darkness and serve as major antagonists in service of a greater evil.
Xezat and Edgar are both scholarly kings who remain humble despite their positions.
Papalymo and Vivi are short Black Mages who wield tremendous power.
Selphie and Yuffie are both the most mischievous and energetic members of their group.
Ramza and Cloud both served in the military and became mercenaries after becoming Defectors From Decadence. Cloud has also appeared in Tactics as a cross-over character.
Angeal and Dorgann both served as mentors to the heroes of the next generation and instilled them with noble values before passing away.
Agrias and Beatrix are both steadfast and honorable knights who were assigned as leaders of all-female units and protectors of the throne and are initially distrusting of the main protagonist, later joining their side after learning of their true character.
Eiko and Iris both harbor a crush on the protagonists, but later accept that their love interest is the one that should be with them.
Garland and Spiritus are both Gods of Discord, with Garland being Chaos and also taking Spiritus's place after his power was depleted.
Fridge Logic
By the end of Arc 1, you can recruit basically a small army of characters. How do they have enough supplies to keep everyone fed? And only two, maybe three characters are known for their cooking ability - do they do all the work to keep everyone fed? Is there enough room on the airship for them all to sleep?
This was answered at last in Act 2. Not only is the airship is Bigger on the Inside and has something Matter Replicators for food, it's noted by the characters that they don't actually need to eat in the world of respite.
Fridge Horror
With all these characters disappearing from their home worlds into this one, who is left to keep their worlds safe from all the threats that are constantly plaguing them? Orience is fighting a war without their trump cards, Class Zero, the world of FFIV is missing basically all of their world leaders, etc. Kind of lends credulity to people like Princess Ashe who are just trying to get home and get on with their initial quests.
In her recruitment event, Krile says she jumped into the Torsion because she heard her grandfather's voice. Her memory of his death was removed when she crossed into the world of respite—but she would have remembered it when she first encountered the Torsion in her own world. Meaning that she thought she heard the spirit of her dead grandfather calling from something that looked a lot like the entrance to the Void.
