Final Fantasy XII/WMG

All or most of the party members are imagined by Vaan.
Vaan is a lonely and introverted orphan whose parents are never seen, and his only friend is Penelo. He spends most of his time killing small creatures in the sewer and stealing from people. The death of his parents and his sad situation have not done wonders for his already questionable mental health. News of his brother Reks' death finally sends him over the edge, and he sets out on a Roaring Rampage of Revenge against The Empire. His lack of personality is not due to shoddy writing, but because he is projecting all of his more interesting attributes as alternate characters, in order to distance his broken and troubled mind from his violent actions. Note that he meets most of his new allies in dangerous spots; when faced with stress and danger he can't deal with, he invents a character to deal with it. You can control all of the characters directly, and to a miniscule degree, because they're extensions of Vaan's mind. This is also why all of the characters have identical license board abilities, except for Quickenings, which are chained together anyway since he's really doing all of them. His sudden badassery at the very end of the game is a result of his mind partially fixing itself since he had just slain Gabranth and avenged his brother, placing his guilt-ridden mind at ease. Vaan is actually an extremely powerful character in subsequent games, because in XII, he was an unhinged, psychotic One Man Army for most of it. He imagined his "friends" fighting, but it was all him, possibly Penelo if she existed, and occasionally Reddas, Larsa or Vossler. Alternatively, one or more (or perhaps all) of the other party members were created by the Occuria to manipulate Vaan and anyone else in the party who is real (if any). It would certainly explain why they were able to interact with other characters. They could have taken on a life of their own when the Occuria gave up on their manipulations. In short, they would be sort of like low-power Espers that were mortal and weren't sealed away.
 * Gabranth does not have a twin brother. Basch is Vaan's personification of his own guilt at being unable or unwilling to serve in the army and prevent his brother's death. He looks like Gabranth, because Gabranth actually did kill Reks, but Vaan believes himself responsible. Vaan literally IS Basch Von Ronsenburg of Dalmasca.
 * Balthier is Vaan's ideal self - exactly the sort of sky pirate he dreams of being. He projects pretty much everything cool or meaningful that he does onto Balthier due to an inferiority complex that forces him to deny any heroic qualities he may have. He says he's the leading man, and he means it. He didn't die when the Sky Fortress went down, because he's Vaan.
 * Ashe is the personification of Vaan's patriotism. The real life Princess Ashelia died, and was probably not nearly as badass as Ashe is, because they aren't the same person. This is why she's always referred to by the nickname.
 * Fran is a hybrid of all the beautiful and exotic women Vaan dreams of meeting as a sky pirate...and possibly his mother. She didn't die when the sky fortress went down, because she's Vaan. Make of that what you will, he's already pretty messed up.
 * Penelo is either A. an actual human with a dangerous fascination with the antisocial thief-eunuch-boy-avenger, or B. Vaan's original imaginary friend, who becomes progressively less important as the other characters are developed in Vaan's mind. The main argument for Penelo's existence is her appearance in Tactics A2 along with Vaan, where the story is not told from Vaan's POV.
 * In Dissidia, he can pull weapons from nowhere and execute awesome magical attacks, becoming one of the best characters in the game.
 * In Tactics A2, he's a brilliantly competent Sky Pirate and an awesome guest character.

The elementals found in the various areas are minor gods sent to protect the fauna of the area.
They are powerful and seem to be made of pure magic energy. They don't like when a magic spell is cast in their area, which makes it seem like they think magic is a threat, especially since they seem to be pure magic energy. They periodically cast protect on the animals of the region. In their bestiary information, they are said to be worshiped by certain sects.

Reddas is half Viera.
There's his skin color, of course, but also look at those fluffy sideburns and the bend across the top of his nose, both Viera traits.

The Jagd areas are caused by Occurian artifacts, and removing them causes the effect to disappear
Supposedly, the Jagd areas are caused by high concentrations of mist interfering with Skystones. However, as Bhujerba shows, it is possible to fly airships in mist/magicite rich areas without interference. Therefore, it must be somethings else that causes skystones to fail, and what is it that sucks up mist? Nethicite.

The three Jagd areas (The Yensa over the Sandsea, the Difohr over the Golmore Jungle/Feywood and the Lumooda over the Paramina Rift) all cover Occurian temples, containing Occurian artifacts (The Tomb of Raithwall/Dawn Shard, The Great Crystal/Treaty Blade and The Stillshrine of Miriam/Sword of Kings). And in two out of three cases, when you remove said magical doodad, the Empire's airships are suddenly flying over there. Coincidence? I think not.
 * The Imperial airships flying over the area are explained in-game as them developing a skystone, based on Manufacted Nethicite, specifically to work in Jagds.

Basch was the one who killed King Raminas and Reks
The Evil Twin excuse was just a contruct of his insane mind after two years in prison. Think about it. He just murdered his king and a loyal subordinate who trusted him implicitly. And as he sits in prison, rotting away, he sees his twin brother, working successfully for the empire. Overcome by guilt and jealousy, he convinces himself it was not him who murdered the King, it was his brother. It makes so much sense. After all, he works for the empire, and they would want to make sure the peace deal does not go smoothly, right? And he doesn't know Reks, so he would have no compunctions against killing him. Anybody who thinks that Basch killed him is obviously mistaken, because Gabranth looks like him, they would think that wouldn't they?

And Gabranth? He plays along with it, because it works with his (and The Empire's) goals.

Viera aren't actually long-lived, they just count years differently in the Wood
As explained by the Viera wayfarer you meet at several points in the game, you can't see the sky inside the Wood, so they wouldn't notice days getting longer/shorter. Also, they are mostly cut off from the outside world. So, the viera have come up with their own way of counting years, which are shorter the Hume years, so people assume they are long-lived when they are in fact not.

The Occuria are the Godhand. Espers are Apostles. The Dawn Shard is the Egg of the Emperor.
Ashe's just the next chosen one. The Resistance (along with the main party) are the sacrifice.. And her Despair Event Horizon? Dalmasca getting wrecked by the battle between the Empire and the Resistance. "All is within the flows of causality"
 * And when the "gift" of Apostle-dom is offered, she tells them to go screw themselves. Bet they weren't expecting that to be within the flows of causality.

The Nethecite is the One Ring.
Cid goes crazy over it, Ashe can't destroy it, etcetara.

Balthier knew all along that the Dusk Shard was Nethicite
He went after it originally to stop the empire from finding it. He could find it when the empire couldn't because he told Fran about it's properties so she could sense where it was. He acted cool about Vaan keeping it because he wanted to throw off suspicion- no-one would suspect some street kid of possessing the Nethecite, so if Vayne found out his true identity he wouldn't beat risk of getting the nethecite stolen off him. And when they got captured on the Leviathan, he let Vaan give it away to continue protecting his cover, figuring that he could steal it back later.
 * This actually would make some sense, as

Vann and Penelo are Self Insert Fic characters.
Everyone knows the REAL protagonist in this game is Ashe, but the game wants you to think Vaan and Penelo are main characters. They are really self insert fic characters for the player and thus have little to no effect on the plot other than to simply be there.
 * Except Vaan is important to the plot, otherwise the entire game would have gone differently. There's a big difference between not liking a character and that character being pointless. Jolee Bindo, Juhani, Mission Vao, Zalbarr, essentially everyone in KOTOR besids Carth, Bastilla and Canderous can be written out of the game, there jobs replaced with keys and you lose nothing. But those characters are beloved. In the same vein Penelo could have been replaced by a really shiny rock. Bangaa headhunters take Shiny rock, Vaan wants Shiny rock back, browbeats Balthier into giving him a ride. Shiny rock gets passed around and winds up in Larsa's hands. Or hell a talking sword works to if you need Penelo's dialogue.

The Occurias real objective was to stop the Moogles for taking over the world and the world changing event between FFXII and FFT is a huge cataclysmic war pitting Moogles against Occurias.
It is quite obvious that the Moogle should be by far the dominant race of Ivalice: They are everywhere, they are the main source of technological advance of the world (when people want to talk about Technology in Ivalice, they just say "Mooglecraft") and they are also quite essential for the economy (ruling Chocobo services, Clans, working in shops), plus, we know that they are at least as deadly as the other races on the battlefield (and they are even worse once they start using their own gadgets). So the big question is: Why isn't Ivalice the World Magitek Empire of the Most Mighty Mooglekin? Answer: The Occurias. The Occurias realised long ago that the Moogles would become the dominant species, and the whole process of choosing a dynast king was intended only to give a Hume lord the power to rule over everyone, including the Badass/Tech-savvy Moogles, while creating "stable" empires that would remain as technologicaly stagnant as possible. The Occurias figured that Moogles would be more tolerant toward the rule of big klutzy not-so-bright but mostly friendly Humes than toward the rule of arrogant noncorporal beings who enjoyed playing God. Then Vaan & Co learned the truth. Vaan is a member of Clan Centurio, remember, and after ho so many hunts done for the clan, chances are that by the time the team learned the truth, he had the ear of Mont-Blanc, so what follow is easy to guess: Then war is all but inevitable, and the Occurias, having ran out of options, decide to immediately go nuclear against the mortals: a tragically untold war of gigantic proportion engulf the world as the Moogles are leading the other races against the Occurias and as the Occurias are indiscriminately scorching Ivalice in a last ditch of spite. Eventually, the Moogles commit a specie-wide Heroic Sacrifice throwing everything they have against the Occurias, and the resulting world is the Ivalice of FFT and Vagrant Story: a damaged world where ancient magics are still there, uncontrolled by Humes who never where able to reproduce the craft of the now extinct Moogles.
 * A) The information about the Occurias' plan goes viral on the Mognet. The Moogles become understandably pissed to have been along with the other mortal races the unwitting pawns of the Occurias
 * B) The Moogles raid the Bahamut, Draklor Laboratory, and every place where there can be informations about Nethicites and Occurias Crystalcraft. Being the uncannily bright furballs that they are, the Moogles quickly find a way to reverse engineer the Occurias magitek.

"The Wood" is actually an Occuria.
It's all a ploy to keep the Viera under control, especially when one considers their sensitivity to the mist.

Balthier is the result of Fran's Husband Husbandry.
While the game is very low-key when it comes to romance, Balthier and Fran behave like an old married couple, understanding each other with half told sentences (look at they're conversation in the Jungle) and having obviously a lot of shared experiences, implying that they have known each other and possibly been intimate, for a very long time. Yet, Balthier being only 22, this would mean that the whole affair would have started when he was a teenager, or even before that. So maybe Fran did Groom Balthier (who was virtually parentless from at least age 14) to make him her companion. Then the romance between the two characters was downplayed when someone at Square Enix realized that the MoralGuardians would probably start a huge fuss if it became apparent that one of the main character of the game Shota's tendancies were too obvious and partially vetoed it.

Vossler is a bastard prince.
Well, look at the Dalmascans. All pale haired, fair skinned with a tan. Vossler looks naturally that colour, in that it is his skin tone, and his hair has a very dark-dusty quality. Who else has that? Al-Cid. Being a 'son of Dalmasca' it's likely he has Dalmascan blood and can't be pure Rozarrian at all (if it is indeed a racial trait to have hair and skin like that). Yet, with Basch being so loyal and so high up, he may as well be Dalmascan, so that wouldn't be an obstacle. His resemblence to Al-Cid is astounding, but due to having Dalmascan blood he can't be fully Margrace, and won't have the name, and being a bastard he also wouldn't have precedence over Al-Cid for the Rozarrian throne. That he never mentions it might be shame or just not feeling it relevant, considering himself fully Dalmascan. Just food for thought.

Basch wasn't actually held at Nalbina to silence Ondore.
Or rather, he was, but it wasn't the primary reason he was there. He says aboard the Leviathan that he knows the Dusk Shard's location, something Vayne's been trying to ferret out through various means for the past two years. It isn't such a stretch to imagine that being the actual reason Basch was kept alive and tortured.

Penelo is incredibly sycophantic.
Yes, in town areas we automatically control Vaan. However the first time we do it Vaan is alone, and later Vaan is sent on errands by Balthier and Basch. It is then heavily implied that actually this is not a case of Party in My Pocket, but that anytime we get to a town the grown-ups hit the bars and send Vaan shopping. So where's Penelo? Well, she actually prefers to suck up to the heroes than accompanying her friend.