But if the first two were so good, why was the third game, Dark Dawn, so poorly received?
I believe this is for two major reasons. One is that the DS entry tried to rest on its laurels, echoing plot and character development from the original duology and riding its coattails in a way that felt bland. Your characters are the children of the characters from the first two games, and constant reference is made to that fact, taking the spotlight from the protagonists and splitting it between them and their parents, causing neither party to shine as brightly as the two from before. This leads directly into the second issue, which is that Golden Sun was released on the GBA during a time when quality RPGs were scarce on the system, and when the concepts it was introducing were progressive and unique. Without the novelty of the elemental motifs and gameplay design, the game felt like a grey echo of its bright and cheery predecessors (which is ironic, as the literal color palettes used in Dark Dawn were almost too bright. But, I digress.)
I believe that Golden Sun was so enjoyable not only because of its mechanics, dungeon design, and simple but appealing narrative, but also because of the environment in which it was released. The reason the simple narrative was able to remain endearing was because it was carried by the novelty and newness of its design, and when the third game is a retread of that, the narrative simply can't stand as strongly on its own, especially when it's diluted by introducing eight new characters in the span of a single game, unlike the gradual introduction of the two distinct parties of the first two entries.
I still want a fourth one, though. Dark Dawn ended on a cliffhanger, and it seemed like the plot could become promising. Maybe someday...?