I'm going to have to go with the Lost Age. It's world was much more detailed and had much more content then Golden Sun, which I always felt was incomplete (although, Camelot practically forces you to play the sequel with the cliffhanger ending). I also believe it has the superior soundtrack, Sakuraba rules, etc.
My only gripe about the game would have to be the Transfer feature. Not everyone has two Gameboy Advances and a GBA link cable. So this leaves most people to input a six-page password to transfer the Clear Data information from the first Golden Sun, which isn't very fun.
Still, I love both games, and would be very happy if Camelot ever makes a third game (it'd be perfect with for the Nintendo DS).