Final Fantasy V/WMG

Gilgamesh didn't die in his Heroic Sacrifice.
We've seen that dying in the Void isn't as permanent as it is otherwise, as the Guardian Tree manages to bring back party members who die in the battle with. Now, when Gilgamesh used Self-Destruct to kill Necrophobe, what it did was rip open a localized hole in the Void, throwing him into another FF world.
 * Considering all the implications that Square's made that all the Gilgameshes we see are the same guy, this is probably canon.
 * But he still can't tell the difference between Excalibur and Excalipoor.

Faris is a cyborg.
This way, whenever she's using the Ninja class and is zombiefied, she's a Ninja Pirate Zombie Robot.
 * You forgot "princess".

The Gogo in this game is the same as the one from FFVI.
Well, if getting thrown into the Void doesn't exactly kill you, then perhaps Gogo was also pulled into an interdimensional portal... right into the belly of a Zone Eater.

Omega is Heartless, but not Evil
Omega is the same 'dragon killer' from the bestiary logs in Final Fantasy XII, and the myriad other Omegas and Omega Weapons seen in the other games, save for FF 10[which is EXPLICITLY Stated as an Unsent, instead of a mechanical/biological superweapon like the others]. Meaning that with each successive Omega model destroyed, a new, more POWERFUL One takes it's place! Followed by numerous self-replicated versions of older models joining it, such as the Prototype and Mech Head enemies. It leads to this factor:

The weakest of the 'Omega' designs is the Mech Head, found in the Sealed Pyramid.

Afterwards came the 'Prototype', from which the Mech Heads evolved, and the spidery metalbug-type Mimics from FF12 are their equivalent to the Mech Heads.

After that came the War MECH of FF 1 fame, an upgrade to the Prototype made much more dangerous.

THEN came the Omega we know and despise from Final Fantasy V, which, upon being defeated, evolved into Omega Mk. II and self-replicated the older Omega Mk.1 models.

The so-called 'Omega Badge' isn't JUST a bragging-rights reward... It's a signal to these new Omegas and their 'leader'[Mark 2] that the player is a MAJOR THREAT!!!!

All in all, if one accounts the side-reports in the FF12 bestiary, the additional notes from the Urutan's entries, it's revealed thatthis thing was designed explicity to do this for one purpose... To hunt and kill an immensely powerful dragon.

In each of the 'episodes' of Final Fantasy that Omega appears, there's usually some kind of amazingly powerful dragon... The first one to be named Omega was 'second best' to Shinryuu...you HAD to defeat it to make t strong enough to fight it's target. In FF12, Shinryuu's counterpart is Yiazmat....so consider this. Omega isn't directly 'Evil' in the classical sense. It's an intelligent superweapon fighting the heroes so that, if it wins, it' ready to complete it's mission and stop a dragon that could DESTROY THE WORLD!!! It's tactics are far from friendly, but it's purpose isn't as evil as being a 'heartless warmachine' would suggest. It has no emotions, it's just being pragmatic for a win-win situation. Kill the heroes and it can kill it's real target. Get beaten by them and it comes back even stronger than before and with a small army of it's weaker model to aid in battle.

The world of Final Fantasy V was the "prime world" of the FF worlds.
The splitting of the worlds birthed more worlds than was assumed; it didn't just create Bartz's world and Galuf's world, it created the other FF worlds. Since the crystals of other worlds were not destroyed, they have yet to merge back to the original.
 * So, it's like Crisis on Infinite Earths?

Gilgamesh is dyslexic.
Or too lazy to actually read the sword's name.
 * Whoever said that the name of the sword is written on it? Gilgamesh just isn't a playable character, so he can't access the menu and check if it's the right sword or not.
 * If Duodecim 012 is anything to go by, and that the only difference between the swords is that Excalibur is red and Excalipoor is blue, then I reckon he must be colour-blind.

Exdeath is Zeromus.
After the events of FFIV, Zeromus's spirit was carried to another planet by the Moon. There it was sealed away in a tree that became Exdeath. That explains why his costume resembles Golbez so much: Zeromus's spirit remembered it.

Galuf's world is in E-Space, at the exact same coordinates as Bartz' world.
Enuo was a renegade Timelord, who tried to take over Gallifrey, and, when he was thwarted, to prevent him from threatening them again, they exiled him to the planet the game takes place on. Once there, he tried to take it over, so he could get back to his home world, so, to seal him away once and for all, the Timelords split the world between the two universes, and banished him to the void between them. Also, "Warrior's Gate" takes place in the Cleft of Dimensions.

King Tycoon was a dragoon in his younger days
Considering his name is Alexander Highwind Tycoon, and that his is named after a kind of spear. You even get the Dragoon Job from the Earth Crystal
 * He also has his own personal wind drake that he rides at the beginning of the game.

The Job Classes were originated by the warriors that fought Enuo.
The crystal shards on the first world contain the spirits of ancient warriors, and the crystals/worlds were split during the battle with Enuo in order to contain the Void. The Warriors of Dawn also use their united powers to have the Crystals seal the lesser evil of Exdeath. To stop Enuo, who was more powerful and had already summoned the Void, a Heroic Sacrifice on a grand scale was in order. Only twelve of them laid aside their weapons to become the twelve Sealed Weapons, just in case they needed to be used again.

The game is Square's attempt at a Henshin Hero work.
Although the Job System is nothing new to Final Fantasy, FFV mixes up the format by having the jobs only activate in battle (as the out-of-battle Freelancer sprites are kept), thus we can conclude that the crystals serve as transformation trinkets. Other elements of the game that make it look sillier than other installments can also be attributed to this.

Culex was Enuo's emissary
That door in Monstro Town is a passageway to the Interdimensional Rift, hence why Culex can visit from another world. He also claims to be fighting in the name of "The Dark Mage", a rather generic category that does not exclude Enuo, and his objective is to consume everything, which is indeed Enuo's current goal (that is, to consume everything with the Void).

Necron from Final Fantasy IX is Necrophobe from this game.
If Gilgamesh wasn't killed by his Heroic Sacrifice and was instead sent through the FF worlds, then Necrophobe probably manages to survive. Note that these bosses, apart from their similar appearance, are both associated with the Void, and are faced at or near the end of their respective games.