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.
Traveling through Konpa Ruins, you can see evidence of a second path requiring use of Frost (or Cold Snap) and Growth. When you find the people you're looking for, Kraden mentions that it was specifically Nowell's power that got them into that part of the ruins... because Rief, when he joins your party, doesn't have either power (yet). This also foreshadows Nowell's skillset for when/if Camelot creates a game in which she's playable.
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!
When you get to Champa, having been specifically instructed to look for her, Chaucha is nowhere to be found. Interpretations vary.
In post-Eclipse Kaocho, you can give a dead grandmother her granddaughter's gift, at which point hers and her husband's souls ascend. So wait - does that mean that, when someone dies, their soul is trapped in their body until someone comes along and frees it?
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.