ON THE SUBJECT OF THE GAME ITSELF, why did the party turn down the Emperor's offer in So R? It seems to me like they just had a petty grudge against the Designated Villain, given that this was not the emperor that committed all those atrocities. Or maybe the Light Emperor is an Unreliable Narrator.
I'll go with "he was an Unreliable Narrator." Given that after the heroes turn down his offer, he immediately declares that "If you do not want eternal life, I will give you eternal suffering!" So, if you don't want to rule together with him, the only alternative is eternal suffering? Sounds like a great guy.
There's also the fact that instead of asking you to forgive him, and understanding that his actions both as a human and as the Dark Emperor were so terrible that you just might not be able to, or not be able to right away without proof of his good intentions, he demands it of you— telling you directly after his flamboyant speech that now you must forgive him. There are a lot of little things scattered in that point towards the fact that even his "good" side is just a different kind of evil— like the entire existence of Mahanon. If you talk to all the people in it, their dialogue suggests that they're basically imprisoned in a kind of purgatory— unable to move on to the true afterlife, stuck in a kind of permanent stasis, and pursued by monsters, and they're desperate to know who or what has put them here. All of that, to me, suggests that Mahanon was created by the Light Emperor, as were the monsters (or directed by him at least, it's suggested that the monsters in the reverse Jade Passage are transformed fallen angels— still, he's not making any attempt to send them elsewhere, and lets them attack the town's residents at will).
And then there's the biggest issue of all: he glosses over the fact of how exactly he became the ruler of heaven, just stating that he "found himself there" after his soul was split. But the fact that there is a palace of the heavens, and a cave full of fallen angels, implying there was a hierarchy for them to fall from in the first place, all raises a very disturbing question: who the hell did he kill/depose to become the ruler of heaven in the first place?
Anyway. Sorry for the rambling on, but all of this is... more proof to me, I guess, that FFII is the most World Half Empty of the entire FF series in many ways. Which doesn't make me dislike it, mind; Soul of Rebirth was the best sidequest I'd played in an RPG remake in quite some time.
Zombie Borghen says that he can't die and that he'll just keep coming back if he gets killed. That being the case, it really depends which version of Zombie Borghen died first; if it was the version in Pandaemonium, he probably got tired of being killed by Firion and his party, and decided to pick on Josef instead. Otherwise, the Soul of Rebirth party probably killed him first, and the Emperor got annoyed at Borghen's constant failures and stuffed him inside that chest in Pandaemonium as a punishment.
What was Cid's angle when the party rescues him from the Dreadnought? He was escorting Hilda to meet up with the party, the both of them got captured, then the two of them were separated and he was imprisoned with "Hilda"(Lamia Queen) for a while before being rescued. Two issues with this: If he knew the princess was replaced, why didn't he tell the party? He's not part of the rebellion, but I don't see him just Sabotaging them. And if he didn't know, how was he kept out of that loop?
Cid could have been knocked out when they were first captured. He could have just woken up in the cell to the fake Hilda, and wouldn't have known any better. Or they were both knocked out, it doesn't change the fact that the swap would have happened while Cid was unconscious. It's always possible that they were separated briefly, and on being reunited, Cid never even entertained the idea that it might not be the real Hilda.
When you fight the Emperor at the end of the game, he's undead. The Blood Sword heals undead enemies and hurts the user when used against the undead. So why is the Blood Sword so effective against the Emperor?
Maybe he's not technically a dead human at that point, but a live demon.
If Ultima and especially Destroy were so dangerous and had no practical use anymore, why weren't the tomes just destroyed? Why bother with the dungeons, Leviathan, and Deumion?
Basic Eastern philosophy. Evil cannot be destroyed only sealed. If it is destroyed then something will replace it to "keep the balance". Often is it worse than before to prevent future imbalance.