What about Dark Dawn? In this comparison to Earthbound, Isaac would get in several years after the release of the latest game in his series, and likely wouldn't get a second character until a new release several installments later (like Lucas in Brawl) when the bar for inclusion is lower than it is currently, because GS doesn't need two reps, as cool as that'd be. So it really wouldn't be until like... SSB6, even though the series will like reinvent itself by then. At this point, even with Dark Dawn, Golden Sun is not really in a position where it warrants more than a single character.
And yes, Golden Sun is generally more popular in NA than the Mother series, but in Japan (which usually gets priority) Mother is a big deal. Like, a really big deal, much more than GS is in America. And keep in mind that originally Sakurai was only planning to have Ness (64), then Lucas without Ness (Melee), and then only when the roster got as big as it did did he have both characters. Also, Ness and Lucas (and other Mother characters) have a lot of popularity in Japan, whereas Isaac is really the only GS character to have popularity anywhere... so without demand, it's unlikely Sakurai would bother adding another character for a series like GS unless GS gets a lot bigger and more popular post-SSB4.