This is what makes Isaac as a DLC character so problematic in the first place. Let's completely ignore the AT and any other Golden Sun content in the game. If you're Nintendo and are choosing characters with the express purpose of selling DLC, why in the world would you choose Isaac, a character from a series you haven't made a new game for since 2010? Heck, why choose Geno, or even arguably Banjo-Kazooie? All you really have are fan polls supporting these characters, while you have actual sales backing things like more Mario characters, Fire Emblem, maybe Minecraft, etc. I don't know what data the people selecting the DLC are working with, but I'm willing to bet it favors the more famous characters over the niche requests.
I know we have some hope that the recent trademark renewal is signalling a new Golden Sun game, but even if we had that, would it be enough? The closest analog there would be Xenoblade Chronicles II, and despite selling well to the best of my knowledge, Rex still only got a Mii Fighter costume. That's also assuming a new Golden Sun would be announced some time within the next year to ensure there is interest in purchasing the relevant Smash DLC, and even if the game entered development immediately after Mario Tennis Aces went gold, that's not all that much development time, and at most a matter of months between development starting and the Fighters Pass DLC line-up being finalized.
I'd love to be wrong about Golden Sun's chances at DLC, but I do worry that, at least for now, all we really have on our side is wishful thinking. The Golden Sun content in the game feels like Sakurai giving us what he can within the scope of Ultimate's development and the expectation of how much attention any given playable character brings to the game. The ballot definitely mattered, but this feels like our peak without either a new Golden Sun game in the near future or Nintendo giving efforts like #GoldenSunday a lot of credit. Maybe we get a surprise in 2019, but as it stands, I think we need to be hoping for a Fighters Pass 2 to get any real shot at becoming playable.