The same can be said of all characters that didn't get added to be fair, priority decides everything in the Smash context. That said, I think it also makes sense within the context of the Ultimate base game lineup. Isaac would have required a proper "new series treatment" that brought along a stage, music, more Spirits, and maybe even an additional Assist Trophy. Only two new franchises were added in base Smash, and Splatoon was too huge to ignore alongside being a popular request (which is an element of Ultimate I think people forget, people wanted the Inklings super badly during the Smash 4 days) and Castlevania got the chance to get in finally after years of also being requested. The only other new stages we got were from Breath of the Wild and Super Mario Odyssey, so that keys us in to just what things were taking priority stage wise (not even Pokemon got a new stage). The remaining unique newcomers all come from more successful and classic franchises as well: Isabelle as the breakout hit from New Leaf and one of Nintendo's biggest characters of the 21st century and Incineroar to bring us a new Pokemon since it's the biggest media franchise in the world basically. Finally we have Ridley and King K. Rool, both of whom were requests that could be added individually without additional content and are from active and beloved series (Metroid Samus Returns was on the way at the time as was the port of Tropical Freeze as extra little bits of recency incentive). There's just not much room for Golden Sun or Isaac in base game. I don't really see how you can drop any of the additions made there.
When it comes to DLC, there's more opportunity, but I think everything in the first Fighter's Pass is now more successful than Golden Sun's entire run at the peak of its popularity. Sure, Banjo & Kazooie are dead, but they had some incredibly circumstances on their side and also were more successful than Golden Sun as well.
I don't even really think with newcomers added to base game Ultimate in addition to what we got that Isaac would necessarily be the first or second in line for those positions either. At the time of release it had been 8 years since Dark Dawn, and that game itself had only released 8 years after its predecessor. The Lost Age sold about half of what the original Golden Sun did and then Dark Dawn sold maybe a 1/3rd of what The Lost Age did unfortunately. It's just in an awkward place despite being a fan favorite... but the sales figures aren't there and I do remember that Nintendo made a fairly big deal about bringing Golden Sun back in the first place only for it to perform so poorly, so they did give it a solid try. Isaac and Golden Sun seem just super dependent on a revival that seems unlikely at this point.
If anything being from his own series would actually help Isaac in comparison to Geno. Like, Geno is hitching to Mario, but only out of absolute necessity and there's probably a fair case to be made he isn't even the most popularly requested Mario newcomer at this point with Waluigi continuing to gain steam and even Toad becoming a more often thought of pick. Like that doesn't put Isaac in a good position necessarily, but he's also not competing with other equally popular options from the same series with more history and "relevance."