Final Fantasy IV the After Years/WMG

Kluya cheated to redeem Cecil into being a Paladin.
Cecil felt bad for a week for killing defenseless villagers. Mopes a bit, suddenly becomes a Paladin, paragon of goodness. Say what? Kluya weakened his Enemy Without considerably; which is why the Maenad was able to reverse the process so much with just a little tweaking.
 * Also, this could only be done with his Lunarian bloodline. Kain didn't get the kid gloves with his test.
 * This might also explain why it took so much longer for Kain, as well as how Kain could do it at all after Kluya spent all of his energy upgrading Cecil. Cecil was cheated in, but Kain needed 17 years of meditation and rumination on his faults and desires before he could change.

Kain got the "Redemption" that Kluya was saving for Golbez.
Note Kluya's dialogue when Kain faces his Enemy Without; he's talking about his sons. The Maenad interference on Cecil's Paladinship included a psychic assault on Kluya's essence. This confused Kluya enough to give the Redemption Test to the wrong person (it helps that Kain was possessed by Golbez when Golbez was being possesed by Zemus, so they had the same psychic "flavor."); but this wasn't what it was designed for; so the test blew up.

The villains of The After Years want to destroy the world because...
...it's been contaminated by the Lunarians. Recall that the Mysterious Girl is pretty single-minded about her mission, but makes special note of Cecil being a hybrid. She also attacks the Red Moon despite it being nowhere near the blue planet at the time. is revealed at the final battle to be an Evilutionary biologist, so this theory fits with his main motivations. As for why this is never explicitly stated: The final boss doesn't expect this part of it's motives to be understood, so it doesn't bother to tell the party.

The Summoner Bloodline of Mist has Maenad ancestry.
Everyone and their brother seems compelled to point out how the Mysterious Girl looks like Rydia. Every single Maenad has Summoning powers. It was noted by Mist townspeople that the Summoner bloodline was genetic; this isn't just something that can be taught; so Rydia was the Last of Her Kind. Sometime in the past; there was a Maenad who went rogue and fell in love with a human living in Mist.
 * Her adopting a Maenad child renews the cycle.
 * This would also be the reason why young girls in general are so much better at summoning. It's not because of any innocence on their part, but because they're the closest to the ancestral Maenads.
 * Somewhat Jossed. Interlude implies that the

Golbez isn't going to take the Red Moon out into deep space again, even if other hibernating Lunarians survived
The Blue Moon kind of just disintigrated. If he takes the Red Moon out, it'll leave the planet below without any tides, which would cause massive ecological disaster, as well as some potential geological problems.
 * Wrong. The Creator's moon wasn't the Blue Planet's other moon, despite being confusingly named "The True Moon". The other moon is still there and can still be seen at the end of The After Years.

All of the worlds from Final Fantasies I, II, II, V, and VI have been destroyed by the Creator
This is why you fight monsters from them. Those enemies are all that's left of our beloved heroes and storylines - if The Creator has been creating and destroying worlds all this time, and the enemies fought near the finale are remnants of those destroyed worlds, and said enemies are from Final Fantasies I, II, III, V, and VI... then I'm sorry, but all the other games had apocalypses just after the end credits.
 * Explicitly false due to the existence of an OVA sequel to V.

The Creator from this game is the same as The Maker from Final Fantasy XIII
The reason he's missing in action there is because Cecil and friends killed him here. Nice Job Breaking It, Hero.

Zemus is controlling The Creator.
A lot of the otherwise spread-out and contrived antagonistic elements of The After Years make sense if one starts to believe that Zemus brainwashed The Creator the same as he did with Kain and Golbez after his defeat in Final Fantasy IV.

Consider that the methods both Big Bads use are extremely similar - brainwashing, collecting crystals using a Dark Knight (in this case, Dragoon, which is not technically the same thing, but still enough), removing the good King of Baron, using the Red Wings to attack the planet and so on - both antagonists were also absolutely obsessed with the evolution of the human race on the blue planet and intent on knocking out the Eidolons and Summoners. They were both using a second moon to stir up trouble on Earth and both can easily resurrect dead enemies like The Four Emperors to do their bidding.

At the end of Final Fantasy IV, Zeromus says, "As long as there is evil in the hearts of man, I will never die" or something like that. When you fight him again in The After Years, he says "Evil is evolution at it's purest!" a telling sign if ever there was one. The Maenad attack The Red moon first. One of them leads Golbez and Fu So Ya down the Lunar Sub - but why? Why didn't she just take the crystals right there? Why did she want to endanger the other Lunarians? She's removing the seal on Zeromus so he can be awakened and take revenge, and he was.

As the crystal also acts as a direct link to The Creator, it's likely Zeromus's link was established when Cecil shone the crystal on him during the fight that killed him. When Zemus recovered enough, he likely exploited Creator's angst of being the last of his kind, dying out due to a painful evolution. Considering the start of Interlude is just a year after, the time frame may be realistic. It seems a bit too convenient that The Creator just happened to go insane around the same time frame and devise a VERY similar plan to wiping out the Blue Planet and the Lunarians. Zemus already knew the power of the Eidolons, so he wanted to take advantage of them for himself this time around. Then he waited and built for 16 years the True Moon, its dungeon, and the Maenad. The first was the Red Moon and Zeromus' resurrection. Then he teleported the Maenad to the Tower of Babil. Finally, when The Creator is destroyed, he "thanks" the party for his destruction - likely for removing his possession and ending him of his long misery.

What hurts this theory is the obvious lack of any canonical/official link between the two and the unknown fate of the Lunarians at the end of the game. While much of the mythos is kinda reconfigured in The After Years and left to the gamer's imaginations, something like that would've been established somewhere in the game.

Nevertheless, the connections, once you see them, are pretty hard to ignore and certainly makes more sense all the way around.