That massive Psynergy Vortex that shows up in The Stinger? It's the Mourning Moon, something that was said near the start of the game to be due for a reappearance any time now — as Isaac's journal states, it appeared every ten years since the Golden Sun event, and when that entry was written, it had already been ten years. In addition, at the beginning the heroes figured that getting rid of smaller Psynergy Vortexes would avert its appearance. Considering the fact that there weren't any to get rid of in Ei-Jei, Morgal, or the Eastern Sea, it would appear that the heroes failed at preventing the overdue Mourning Moon appearance.
Why does King Paithos suddenly start talking about Amiti's family situation to a group of strangers? Because one of those strangers looks suspiciously like Amiti. He's trying to get some answers out of Rief.
Glacial meltwater usually contains amounts of minerals from crushed rocks. Khiren Water is mentioned to be from glacial runoff, and restores PP. It probably contains minerals from crushed Psynergy Stones!
There's a Water-Adept-Only route through the Konpa Ruins... because Kraden was heading that way with two Water Adept companions. Rief doesn't have Frost when he joins the party, but Kraden does mention in the cutscene there that Nowell got them into the cave system, so presumably she does.
Camelot wasn't done with the Fantasy Counterpart Cultures in the original two. The eastern part of Angara (the series's equivalent of Eurasia) is called Ei-Jei, which sounds vaguely like "Asia" and is the game's equivalent to Asia, and the country of Sana, which resembles China, is south of the Endless Wall, which seems to be the game's equivalent of the Great Wall of China. Likewise, in the same game, Nihan is one letter away from Nihon, the Japanese name for Japan, and is the game's equivalent of Japan. (It's even vaguely shaped like Japan; Yamata City is on the island corresponding to Kyushu.) Yamato also was a name for Japan at some point in history. Yamatai is named after Yamataikoku, home of the legendary priestess/queen Himiko.
The beastmen used to go into a frenzy around the full moon and get into fights all the time and stuff. One of the beastmen mentions this, and that Volechek starting having public executions on the full moon to "take the edge off," and then the fights stopped. But the people of Garoh didn't have this problem, and they were basically beastmen precursors. However, they only transformed under the full moon before the Lighthouses were lit, and presumably now they are in permantent beastform. So basically, for beastmen, it's always the full moon with all this Alchemy energy everywhere, hence why they're always in a beastly form. But when you double that energy when an actual full moon shows up, it brings out even more of the beastliness on top of that.
Two regarding the revelation of Darkness and Light Psynergy.
Isaac in the Tanglewood Forest scenes, telling Garet to clear a path with Fireball, explains that the forest is full of twisted "negative energies" that can be dispelled with "light and warmth". During the Grave Eclipse, Kraden makes similar observations about that, using almost the exact same words. They're talking about Darkness Psynergy, they just don't realize it yet. Karis even says in the Tanglewood scene to "remember this, we don't know when it will come up again".
The Cloak Psynergy in the first game involves using dark shadows to hide your party. Yes, they were foreshadowing Darkness Psynergy as early as the first game. It's also of the Mercury element — that is, the element associated with cold, which is mentioned in the Tanglewood scene to be a result of said "negative energies".
Remember the trap back in Sol Sanctum? Sure, the sanctum was associated with the sun, and Mt. Aleph was the epicenter of where the Golden Sun event occured. But it can also mean that apart from hiding the Elemental Stars, Sol Sanctum was a symbolic cage for hiding both the power of the Golden Sun, and the Mourning Moon which are tied with Alchemy, and by extension, hinted at both light and darkness playing a role in Alchemy, possibly moreso than the four standard elements.
Alex received most of the Golden Sun's energy. What kind of adept is he, again? Mercury, which also happens to be the closest planet to the sun. And who got the rest of Golden Sun's power? Isaac. And guess which planet is second closest to the Sun.
Sveta can use Spirit Sense to read the minds of corpses. There's a side quest where this is used to send the spirits of an old couple to the afterlife... implying that everyone else whose Spirit can be Sensed is trapped in this world and unable to move on. Sveta can also Spirit Sense graves where people have been buried for centuries, some of whom were around during the first use of the Eclipse Tower.
Amiti's strong opinions on criminal justice make a lot of sense when you consider how close Ayuthay is to Champa, and how wealthy they are. He's probably had an unmentioned encounter with the business end of Champan piracy in the past.
Rief is from Imil. So, why doesn't he know what Water of Hermes is when you get some from Briggs?
Eoleo, a fire adept, is being imprisoned in a rickety wooden cage with few apparent guards. And yet, he can't escape without your party...
Right by Eoleo, there is a small ledge that the party should easily be able to jump down that would take them right into Belinsk Palace. And yet, they had to take the long, difficult and potentially world-destroying path through the ruins...