Feena and Reah stole the black pearl

Little details scattered around the Ys-verse would seem to indicate that Feena and Reah, far from being wise goddesses, were a pair of rebellious teenagers. Mask of the Sun tells us that the black pearl originally came from Celceta, and the Tabulas from Ark of Napishtim hints that the black pearl is a special Unobtainium called Emelas. They also tell us that Humans + Emelas = Big Trouble, and unfailingly results in uncontrollable monsters. Feena and Reah would either have to be evil or dumb to give this power to a bunch of humans.

So here's the theory: Feena and Reah were teenagers by Precursors standards living in Celceta, and believing that humans should be cooperated with rather than eaten, they stole a big chunk of black emelas and fled to create a Utopia where they could live together in peace with humans. It didn't end well.

Lilia is also a descendant of one of the six priests

When you get Lilia's medicine, her mother gives you the return spell, the magic of Priest Hadal. This apparently had originally belonged to Lilia's late father. Why would a man in Rance Village have Hadal's spell instead of Hadal's heir in Lava Village? Because he was also a member of the Hadal family, from a different branch. This would also explain why Lilia was drawn to the core of Ys along with the Goddesses and the six confirmed heirs. The reason there weren't even more people traveling there is because Dulles was making a deliberate effort to purge the bloodlines of the priests with his sacrifices, and he succeeded in killing most of them.

Kishgal is Tyalmath

In Ys Origin, all of the bosses from Ys I and II are accounted for, except for two: Tyalmath, the boss of Noltia and Druegar, the first boss of Solomon Shrine in Ys II. However, Kishgal—one of the Darklings that you fight on Eunica and Toal's paths, likes to shoot out waves of ice spikes much like Tyalmath. Seeing as Kishgal, Epona and Zava don't die on Toal's (the canonical) path, it seems likely that the demonic influence finally got the best of Kishgal.

Galbalan was created by the Eldeen
One of the bosses in Ark of Napishtim (The second dragon) is referred to as the original Galbalan. This is the name of the Big Bad in Oath in Felghana (Though they don't look anything alike), whose few spoken lines make references to the Eldeen. Theory: The Galbalans were created by the Eldeen, possibly as guard creatures. The one that attacked Felghana was one that escaped and went rogue after the Darklings stole the key to the Ark, causing the end of the Eldeen civilization.
  • This is pretty much confirmed by Oath (Galbie talks about the "Black Ark"), though Napishtim implies that Galbalans are made by humans, rather than Eldeen (They're the Ash Emelas creatures that the Tabulas talk about). As for the difference in appearance, given that Oath's Galbie shares the Large Central Eye with several of Napishtim's bosses, it's possible that there are multiple models.

Dark Fact stole Adol's silver equipment and then left more powerful weapons lying around to trick him
Dark Fact already spends the whole game being fairly Dangerously Genre Savvy, what with hunting down every last piece of silver he can get his hands on prior to the start of the game, and then confiscating Adol's silver equipment at the first opportunity. So it seems a bit odd that he'd just leave powerful swords and equipment lying around Darm Tower...unless that was the plan. Obviously the player would want to use the most powerful equipment they can find, but since they need the full set of silver equipment to even scratch him, and the player can't trade out equipment during boss fights, it'd make sense to leave equipment in plain sight with technically higher stats, but are still effectively worthless. And he would've gotten away with it, too, if it wasn't for that meddling Reah.