The game pulls a Nonstandard Game Over if Isaac refuses to take on the quest of saving the world. The screen goes to sepia and the game intones "And so the world drifted towards its fated destruction." Bit of a downer there. But wait, there's a problem with this whole thing...if Isaac refused the call and stayed in his little village...with the Mars Star, which the villains were unable to wrest away from him before Mt. Aleph's eruption forced them to escape...why would the world be headed towards destruction, when the villains were trying to light the lighthouses and thus would have needed the Mars Star? That's when you realize that the designers had always had the entire plot of both games — the first game and The Lost Age — figured out, including the part where lighting the lighthouses and restoring Alchemy to the world would actually save it from destroying itself, and this was a case of extremely subtle Foreshadowing that barely anyone would have picked up on.
The Wise One doing... something to the Mars Star even before that is another great example of that kind of foreshadowing, the kind that doesn't pay off 'til the end of the next game.
The games were split because the developers, in all their ingenuity, wanted to explore the idea of playing one half of the game with the heroes, and then playing with the opposing party in the next game. On top of that, it becomes doubly brilliant when you realise that in doing so, the games basically Deconstructed the traditional concept of Black and White Morality, which is so often prevalent in fantasy fiction - not only were Saturos and Menardi trying to save their hometown and by extension, the world, but discussions between Isaac and Felix's groups after Jupiter Lighthouse reveal that the very reason they invaded Sol Sanctum in the first place - setting off the trap which released the boulder - was because the village elders of Vale refused to believe them when they tried to explain the danger Weyard was in! As a result, they partially brought the boulder-day disaster upon themselves due to their stubbornness and mistrust, albeit indirectly. It's quite extraordinary how the game makes such a subtle element of Grey and Gray Morality, which serves to anchor it to reality just a little bit more than most fantasy-based stories. And considering the plot of the first Golden Sun was already praised for its complexity before these revelations were made in The Lost Age, it's no wonder so many people deeply appreciate this game's storyline as much as its gameplay (complaints about lack of highly-developed characterisation aside).
The Kimbombo Mountains region have a few water puddles at important locations—characters can use the Frost psynergy to freeze these into pillars of ice in order to solve puzzles. For the purpose of the Stealth-Based Mission the first time the player comes through, these puddles don't have a point—the party doesn't have a Frost user at the time. On the way back with Piers (who can use Frost) in the party, exactly one of these puddles is useful (to get a djinn), but the others don't matter because all of the guards are gone. For the one pillar that the player can make, well, it leads to the djinn, a shortcut back, and...a route back down to the puddle. Most players didn't even notice the uselessness the first time through the game, but it can be annoying the second time because while there may be times in the game when using a particular psy power is pointless or even detrimental to solving a puzzle, it's always part of a puzzle where using that power in the right way is part of the solution. However, there's a reason for it: The level designers did need to make a way through that relied on Piers since he was supposed to have snuck by ahead of the player's party. Since he lacks the Move and Whirlwind psynergies that the party needed for its route, there'd have to be another way—one that used only Mercury powers. It also explains the pointless route back to the useful puddle—though the party would have easy access to the puddle coming back from Kibombo, Piers wouldn't unless there were some vines to climb down the the puddle so that he could freeze it from his side.
By the same token, there's the Gondowan Cliffs. Felix's party needed to make use of Move, Lash, and Scoop to open a path across, but upon entering from the Indra side, most likely the first thing you'd notice is the puddle conveniently located between two ledges. You have no use for it at the time, but it, too, was put there to give Piers a route through the cliffs. If you come back after he joins you and try taking that route, you'll find that it's indeed possible to get through with no Psynergy other than Frost (incidentally, just like the other route, you need to use Frost at one point along this route to get a Djinni later).
If, during the part of the game where you sneak through the Kibombo Mountains, you try to approach the first puddle, you'll get spotted by the guard. This seems like it'd be impossible for Piers to get through, then... However, when the two guards are talking before this, one mentions that guards had been found knocked out around the entrance before. If the guard in that spot was knocked out, then Piers could definitely reach the puddle unnoticed, and it also explains why the Kibombo know that someone else had already tried to sneak through. They really did think of everything!
There is a river in Russia labeled Kolyma. Kolima is a town in the game. Then a city called Bilibino - Bilibin is another town in the game. In the second game, there is the Arafura Sea - the town called Alhafra would be arafura in the original katakana - and Izumo,probably others. The continent of Angara kind of looks like Eurasia, and the locations of Kolima and Bilibin fit that assumption... but Gondwana was a place in India, and the continent of Gondowan looks like South America and is south of Angara. Furthermore, "Gondwana" is also the name of one of the supercontinents from way back and just look where South America used to be. The world of Golden Sun is ours in the past! ... and also flat. So, about that problem they have in Prox, in The Lost Age... is it really that the Falls are eroding the edges of the world, or is it the land that's moving out towards the falls ?
A lot of players were wondering about how Felix, Felix's parents, and Kyle could all have survived getting a damn boulder dropped on them, exactly. Watch the scene in Kolima again: Remember how apparently Adepts have a defence mechanism built in in the form of those Psynergy shields that kept them from being affected by Tret's glamour? If all Adepts have that, then there's no reason it couldn't have saved Felix et al. from a boulder. Incidentally, this could also account for Alex surviving the end of The Lost Age.
Ivan's theme, "A Little Friendship", plays in the scene where you meet Hama and she teaches Reveal to Ivan, along with a little about Jupiter Adepts. The cutscene's focused on Ivan, so it's only natural that his Leitmotif plays, right? Except that it also foreshadows that Hama's his sister.
Near Champa is Treasure Island, the resources of which are being used by the people of Champa to restore their economy so they don't have to depend on piracy any more. Felix & Co. can find and loot the place, and are even encouraged to do so by the presence of a Bonus Boss and summon tablet there, which seems like you just indirectly robbed Champa. However, the point where you stop finding empty chests and start finding the ones that have stuff in them is the point where you actually start to use Psynergy to reach the latter ones. Felix and co. weren't robbing Champa since they wouldn't have been able to reach those chests in the first place.
Briggs, when you fight him, has a weakness to all four elements. Mostly unnoticeable, since it's only hinted at by punctuation. But when thinking about it, it's totally understandable that he is weak against any form of Psynergy, since he actually can't see it, being a non-Adept.
Saturos and Menardi, the Mars villains from the first Golden Sun are thoroughly hated by players of the first game, even after learning about their true motives on the sequel. But still, that hardly justifies their ruthlessness and their smug attitude. So what justifies Saturos's group attitude, resorting to even terrorism and kidnapping - something that their successors, Agatio and Karst, were against, despite briefly crossing the Moral Event Horizon by triggering a trap on Isaac's group, something that even they lampshade as being dishonorable, but necessary - in order to ultimately save the world? The fact that Alex could have gained their collaboration by filling in full detail what bounty awaited for those who awakened the Golden Sun event. So, to them, saving the world was merely a consequence for acquiring a greater power. Why were Agatio and Karst acting somewhat more chivalrous? Simple, the Proxians had already helped Alex in where he alone could fail, and with Menardi's death as a token to motivate Karst's help, he could seize the whole Golden Sun for himself, instead of splitting it with two others, and so no word about that event was said. While this is all conjecture, it sure as heck seems to corroborate a few character quirks from these four misunderstood villains.