So I played through this again and just wanted to comment on the story again.
And to help prevent spoilers, even though everyone should know this by now, I'm spoilering it.
[spoiler=Story Stuff]
So playing through again, I realized just how much that Alex had manipulated everyone. He knew that the Insight Glass would be given to someone from Ayuthay, and he knew that the Alchemy machines would be necessary for the activation of the Apollo Lens. So he reactivated the Alchemy Well (but not the Alchemy Forge since he is still a Mercury Adept) and fathered Amiti, and then vanished without a trace. Along the way, he allied himself with the Tuaparang and began to manipulate them in order for his ultimate goal. So the Eclipse Tower was activated, which was necessary to release Light Psynergy when the Apollo Lens were fired at it. My guess is that he was in Belinsk when the explosion of Light Psynergy occurred and then left promptly. He also was manipulating the Tuaparang because only with their Dark Psynergy would the Apollo Lens be activated (knowing full well that through manipulating Volechek into reactivating the Eclipse Tower and having to be saved by the Dark Psynergy would he be able to fire the Apollo Lens and not cause the death of any of the party members, allowing them to be alive when he needed them again).
In summation, I'm guessing that Alex is gonna be the final boss of the next, and probably last, Golden Sun game. Looking at all the hints in the GBA games for this one (Takeru, wider world, massive global restructuring, slower aging for the Warriors of Vale, etc), showing that Dark Dawn had been planned all along. Not only that, but the mystery of the Psynergy Vortexes and the massive one shown at the end of Dark Dawn (coupled with the final text of The End...?) show that there's at least one more Book to the Golden Sun saga.
[/spoiler]
That make as much sense to anyone else as it did to me?