I never really gave it too much thought, though. In the last year or so, HCBailly did LPs of Golden Sun and The Lost Age, and I just finished rewatching them the other day... and it occurred to me that these two games were originally meant to be one huge game, but was split in two, likely due to issues with cartridge space and time constraints. This is mostly down to the fact that there are placeholders for both items and Djinn that are in Golden Sun which translates directly to counterparts in The Lost Age. Beyond this, the map from Golden Sun is still there in The Lost Age, but devoid of all towns and dungeons except for Mt. Aleph and the Lighthouses (none of which are actually accessible).
Dark Dawn takes place 30 years after the end of The Lost Age, and much of the world has changed. Entire continents have shifted, and the terrain is all very different from before. The Golden Sun caused a lot of devastation throughout the world in the process of reviving the power of Alchemy, and it caused many features to appear, disappear, or move outright. An example of this is Kolima Forest and town, both of which physically moved further northeast, the forest into the mountains and the town to the base of the mountain. Apparently, the town moved directly on top of a swamp, which wound up causing issues later, during Dark Dawn. The Golden Sun event caused the reappearance of Beastkind, a humanoid race of people with animal features which mostly lived in the Kolima area. The Kingdom of Sana conquered them, so they rose up and struck when they could, forming their own nation with the newly built Belinsk as the capital. Due west of their, Bilibin rose to their own nation as well with McCoy as its ruler; the border between the two is a place of contention.
The arrival of the Golden Sun caused many things to be uncovered, such as the existence of many Alchemy machines throughout the land. People are apparently predisposed to settle on or nearby these Alchemy machines, thus why Ayuthay, Kaocho, and Passaj are where they are. Most of these machines are entirely beneficial, owing to the fact that ancient cultures were mostly peaceful and desiring to advance the science of Alchemy. This shows in how the Alchemy Well creates a spring of water for one town, the Alchemy Forge allows for amazing works of engineering, and when the two are working together, pump large quantities of water to an entire region, preventing the place from becoming a desert.
On the other hand, there are Alchemy machines that do not have beneficial results, such as the Alchemy Dynamo that Belinsk was built on top of. This was a machine to activate the Eclipse Tower, which apparently had power over the moon to force an eclipse that caused monsters to run wild. This was likely an example of the power that Alchemy could wield to perform evil, and amongst the reasons that ancient culture decided to seal the power of Alchemy away, not knowing that doing so would cause their world to crumble and die. Apollo Sanctum was clearly built to combat the Eclipse Tower, though whether it was used back then to put a stop to the disaster, or only built but not used before Alchemy was sealed is currently not clear. One thing that is clear is that after Alchemy was sealed, all of the old Alchemy machines were sabotaged so they would not work should Alchemy be unsealed.
The Wise One, a living Philosopher's Stone, was likely amongst those that made the choice to seal away Alchemy. This is clear from the way that there are Wise One statues scattered about the world in Dark Dawn that restores your characters when you examine it. Between that and how it appeared in Sol Sanctum after the Elemental Stars were stolen, we see a being that has made it the sole mission to prevent the unsealing of Alchemy. It's hard to tell if The Wise One knew the world was dying due to the seal on Alchemy, but it made its choice on that matter when it charged Isaac and Garet with preventing the lighting of the Elemental Lighthouses.
There's still a lot of unanswered questions, including what's going on with the Psynergy Vortexes, who the Tuaparang are and what their aim is, what is Alex playing it, and what really causes the Mourning Moon every 10 years. Golden Sun is a series with many years between titles, and I think we are due for a new one, especially given how Dark Dawn ended. There is hope for a new game, given the rumors that Isaac made it into Smash Ultimate, but I'm not holding my breath. If, and this is a rather massive if... if a new Golden Sun comes out and it's only available on the Switch, I MIGHT get one for that. But again, that is a very, very big if.