In terms of game balance? Golden Sun is definitely the best I've seen. Thus far, it's the only one which Smarties hasn't found a way to break the heck out of, and that's already saying something. I also like the class change/summon system (and how using your biggest source of damage turns your characters wimpy and vulnerable for a few turns), and the overworld graphics with the little emoticons did amuse.
Storyline...eh, it's decent enough. Not anything devastatingly original, but at least they put some effort into giving the characters personality.
Really, my only main gripes would be: one, the monsters are about the most boring thing ever. There's just a very limited amount of sprites with a bunch of recolors to them, and in both games the big bad end boss was a ginormous dragon. D= Plus, the sprites look very grainy and pixelly most of the time. Also, the attack names were highly repetitive and often incited WTFs as well. (I mean...what's with those 'blessing' things all hurting you? x.O) Also, there's a bit of aimlessness to it (terrible if you forget where that last non-repeatable piece of dialogue wanted you to go D=) and traversing that huge world map while constantly being harassed by freakin' sea monsters is seriously annoying. >.<
Overall, they're both good games, though, and some of the very rare kind that doesn't get ridiculously easy by the end of it. Good? Certainly. Best? I'll have to pass on that one because my knowledge on the subject isn't wide enough. =O