I like playing good guys. If you look at the Golden Sun games, you spend the entire first game chasing after Saturos and Menardi and fixing everything they broke. The Altin Mines, the trees in Kolima, Silk Road, etcetera. Then, in The Lost Age, you play as Felix. And you spend the entire game breaking stuff and taking people's things. You steal the Great Gabomba's magic, you try to steal the boat... You only rarely help people out (yay for Izumo). Isaac is just a better person than Felix.

He also has a better battle theme, which is also important.