I envisioned said story following Isaac and co. rather than any other character and the premise steams from what Kraden said at the end of The Lost Age. That of course, being the dangers associated with the re-introduction of Alchemy to the world of Weyard and fears of nations building armies of adepts, ushering the land to war that the wise men mentioned in the prologue attempted to prevent.
And honestly, I believe this would have been the angle Camelot went with if they made GS3 around 2005-2006 rather than 2010. It would have made a lot more sense.
As for the antagonist, it really should be Alex because TBS and TLA builds him up as an imposing, manipulative figure and we go through all the games without actually fighting him. And worst of all, we don't even know why Alex seeks the power of the Golden Sun and what caused him to be the way he is. Maybe this hypothetical GS3 could really get to the nitty gritty of all that and have a final face off where Isaac & Felix go face to face with Alex in the last boss fight.
*insert Thanos snapping his fingers here*