You also left out something in regards to Golden Sun's ending.
The Wise One asked Isaac to put the Mars Star back where it was, and then had him take it out again. This gave Isaac some of the Golden Sun's power way before the main story kicks off, which also meant Alex could not achieve full power. The Wise One tricking the heroes wasn't so much of a trick, but a test to see if the kids really do believe what they were fighting in and if they would accept the responsibilities that would come with it. That is why he turned the heroes' parents into a three headed dragon and it was nearly slain by its own kids. Isaac knew what had to be done, even if it meant nearly killing his parents to save the world.
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