Ooh, that would actually he a tough call between Golden Sun and Tales of Symphonia... Both for their story and gameplay. I suppose, ultimately, I'd have to go with Golden Sun because it was the first game I ever played that had
The antagonists from the first chapter who you were told by the elders of you village were out to destroy the world were actually going about saving the world. The only reason they set the plot in motion in the first place was that their village was literally going to fall off the face of the earth unless they lit the elemental lighthouses and returned the power of alchemy to the world.