I personally liked the story in the original Golden Sun the best.
It was basically a chase story all throughout, and for that reason, every advancement I made on the map felt like I was advancing the bigger plot at large, since Isaac and Garet's main mission was the capture of the Sanctum thieves, and the rescue of Jenna and Kraden. I loved how the story would show how Saturos and Menardi were always one step ahead of you with the destruction they'd leave behind, and the NPCs that'd mention how they'd seen this strange pair having passed through a village or elsewhere. Plus I recall there being a place where a kid was turned into a tree and stacked on top of other kids turned into trees. Saturos and Menardi knocked them over when they passed by. If you don't rescue that tree that fell into the water before you turn them back to humans, the kid dies. T_T I always felt engaged with the story of the original.
The Lost Age didn't quite feel as immersive and engaging, story-wise, to me. Felt like over half of it was a side mission, and the lighthouse mission was largely postponed. I don't recall feeling any sense of danger or tension in the story either. As Felix, we had an alliance with the villains, and Isaac+friends were clearly good guys and if anything I was dying for the two parties to meet already so Jenna can explain everything because obviously Isaac and Garet are going to believe her, if not Kraden. Plus I thought a certain spoiler kinda hurts the feelz that the original's prologue left.
But I still enjoyed Lost Age. The game-play was certainly better! Better dungeons, more classes, psynergy, puzzles, summons, non-linear exploration, etc.