The GBA has the world's best turn-based strategy collection, hands down. But unfortunately it's a little lacking in truly excellent RPGs. Your daughter was right to call Golden Sun only 'okay', it was pretty simplistic despite great graphics and sound.
Sword of Mana is an updated version of the first of the Seiken Dentetsu series, which came to the US first as Final Fantasy Adventure, and later as Secret of Mana, then Legend of Mana. We missed out on the third game in the series, which is a terrible shame, as it's pure gold. Sword of Mana is great, but an important thing to bear in mind is that it's a real-time combat like Legend of Zelda, and not turn-based like the 'traditional' RPG. Dunno if that would make a difference to her or not. One thing to note though is that it has a female protagonist that can be chosen in place of the male, and she actually has a different storyline than he does. That could hold extra appeal for your daughter.
Lufia is mediocre, and the Phantasy Star Collection, while harboring fond memories from the old-school, would surely not appeal one bit to someone who grew up with more modern games. The Mega Man Battle Network series is fun, but can get repetitive in short order, on top of not being fantasy in any way, shape, or form.
Mario and Luigi is a pretty fun little game, but in my opinion not as good as the original Super Mario RPG. And also not really fantasy, though it is in a pretty fantastic world.
Pokemon and its thousand copycat games can be pretty safely skipped over by everyone. I'm fond of the Pokemon series of video games, being something of the pioneer of a neat idea, but still don't hesitate to call it all very formulaic and over-simplified, even for a kids' game. The GBA Pokemon is a signifigant improvement over the older versions in graphics, sound, and variety in the monsters, and even lets you choose between a boy and a girl for your character, but even with all of that I wouldn't recommend it for someone who'd played through Golden Sun.
The strategy games, Advance Wars 1 and 2, Final Fantasy Tactics, and Fire Emblem are all absolutely wonderful games. Final Fantasy Tactics also has a very nice storyline to it that should appeal to an RPG player despite its squad-based combat system.
It has elements from both Paper Mario and the original Mario RPG from the Super Nintendo days. It's really fun AND funny!
