I agree to an extent, which is to say raw numbers won't tell us the whole story. But let's be real, people can be a fan of multiple things at once. Just because someone didn't vote for Isaac in the Smash ballot doesn't imply that they can't be Golden Sun fans.
But as to your point about mindshare (is this even a term? I'm not familiar with it), I would agree this is largely due to advertising, or more to the point the lack thereof, on Nintendo's end. They chose to push Fire Emblem, and it worked. The same can't really be said for Golden Sun. Now again there are almost certainly other confounding factors at play that we aren't privy to, and this is also assuming the numbers we have access to are accurate, but I have to believe that Golden Sun would be much more prominent today if there were an actual serious push for the series on Nintendo's end. My suspicion is that based on some factors that we don't know, Nintendo deemed Fire Emblem to be a series more likely to grow into greater success down the line, perhaps because it filled a niche that Nintendo wasn't covering with their other IPs, and as such made a marketing push that doesn't immediately make sense to us based only on the numbers we have access too. Still, it's unfortunate, and mildly irritating, to see a series that you love get ignored in favor of a series that seems to have been performing worse.
Also when it comes down to it, the fact that Golden Sun appears to be much more popular in the West likely led to it being a lower priority for Nintendo as a whole. In general seems that the company as a whole is much more interested in increasing the popularity in the West of titles that are already popular in Japan, rather than the other way around.
Having said all that I still hold a sliver of hope that the very obvious push for more Golden Sun will spark, in the very least, a discussion at Nintendo as to the future of the IP. Given the fan reaction to games like Octopath and the general reception of RPGs on the Switch I feel there is a non-outside chance that Golden Sun could be considered for revival in some fashion. And at this point, that's what I'm hoping for.
In completely unrelated news, the Assist Trophies I would upgrade are:
1 Isaac
2 Bomberman
3 Tingle (if we have to choose Ultimate ATs replace him with Skull Kid)
4 Ashley
5 Takamaru
Waluigi would be fine too, but he doesn't excite me at all. Overall I really really want Isaac and Bomberman, the others would just be gravy. Tingle is a big want as well, but I'm not sure if he fits the criteria, and even if he does I have very little hope of him actually happening anyway.