I dont even know if this makes sense I know the first Golden Sun sold and reviewed well, but Mother and Xenoblade have a this is something special mystique that Golden Sun doesnt. It just doesnt feel like a big enough deal to get a character. Its not retro, and its not currently active. It would seem strange to introduce a minor IP into Smash Bros. 14 years after its peak relevance.
I feel the same way, too. Ever since the idea of Shulk possibly getting into Smash Bros. became very real due to the Gematsu leak, I've sort of compared Xenoblade to EarthBound, and Shulk to Ness. Neither are very popular franchises or characters compared to other franchises and characters in Smash Bros., but there's just something special about them. Even if you haven't played them, you can tell that there's something special about them by how they're revered those who have. It's like, you just know that these games, while ultimately niche, will no doubt be timeless classics and will go on to be great influences. I think it's safe to say that that's definitely the case with EarthBound, and while Xenoblade is still relatively new, it seems to be heading the same direction, too.
Golden Sun, on the other hand, hasn't really been received in quite the same way. It was certainly popular on the GBA, but it kind of seems to fall more in line with other Nintendo franchises like, say, The Legendary Starfy or Fossil Fighters to me, though it's probably more popular than any of those. But it just doesn't stand out in the way that EarthBound and Xenoblade do, if that makes any sense. And to be fair, Golden Sun is one of the few Nintendo franchises that I haven't yet played, so I may not be able to analyze it the best, but just by going off of how the different franchises are received, I think it's pretty clear.
Also, another thing that may have helped both Ness and Shulk get into Smash Bros. is their connection with the development of the Smash Bros. games. HAL Laboratories worked on both EarthBound and the original Super Smash Bros. It wouldn't surprise me at all if that is the main reason why Ness got in, because the people working on the game were close to EarthBound and pushed for it. Shulk's situation isn't exactly the same, but Monolith Soft did help develop Brawl, and they released Xenoblade a couple years later. I know it probably wasn't the same Monolith Soft studio that developed Xenoblade, but there may have been some key people who made connections with Sakurai, which may have helped lead to Shulk's inclusion in the next game.
I think it may come down to both the "specialness" of those two franchises plus possible developer ties to the development of Smash Bros. that got them included. Sakurai has strict guidelines about which kind of characters can be included, but we know he'll make exceptions, like how Snake was added at Kojima's request. Like Ness and Shulk, Snake isn't a character you'd expect for Smash Bros., for different reasons (Ness and Shulk due to popularity, and Snake due to, well, third-party status and not having the strongest history with Nintendo), but those characters all made it in against the odds due to being "special," I think. Snake may not be quite on par with Sonic or PAC-MAN in terms of being iconic (not that he's not iconic at all, of course, just not quite at the same level), but I don't believe Sakurai would have added Snake in Brawl if he didn't think there was something special about him. Same with Ness and Shulk.