I feel like Isaac's chances are super up in the air and depend on several sort-of independent factors. Let me explain:
1. If a new Golden Sun is development. We have several things that point to this: Aces' development ending in mid-2018, the trademark for Golden Sun being applied for soon after, the GS reference in (the Japanese version of) Aces, the Takahashis' insistence on wanting to make a new RPG, general fan demand, etc. However, none of these are solid confirmation, which sucks. A new Golden Sun would greatly help Isaac's chances.
2. How visible Isaac's fan demand is. We know from Ridley, K. Rool, and Banjo that Sakurai will take fan demand into account. However, we also think that he was surprised by K. Rool's demand, which is strange, due to K. Rool's popularity all over the world. If he didn't know people wanted K. Rool, how will he know people want Isaac? (This leads me to my next point...)
3. How well Isaac did on the Smash Ballot. We can assume he did at least decently well since a ton of Golden Sun content was added to Ultimate. However, he didn't quite reach the ranks of K. Rool or Banjo, the only characters that I personally feel confident in calling a "Ballot Pick". (Sakurai includes Simon and Ridley as Ballot Picks, but I don't really believe that. Ridley was just general demand, and Simon didn't seem very popular according to exit polls.) Additionally, NoA was surprised by the backlash to Isaac's Assist, which means either NoJ didn't share the Ballot results, or Isaac did worse than we thought. (This is really suspicious to me, because it seems obvious that NoA would be scouring Nintendo-related boards to check in, and they somehow missed us?)
4. Will first-party characters be DLC. This seems obvious to people like us, but it's no guarantee that Sakurai will spring for the seemingly obvious picks like Waluigi and Isaac.
5. Finally, will they upgrade Assists? We have no clue on this one. I think the real question is "How far will Sakurai go to please fans, and were we loud enough when it mattered?" The Isaac/Golden Sun is kinda notorious for going quiet for a while, but we've done our best to stay relevant this time around. If Sakurai really wants to please the fans like he said he did, Isaac should be at the top of the list (or near the top, at least). This is the biggest one to consider, in my opinion.
In conclusion, it all really comes down to Sakurai and his judgement. If he feels the Golden Sun fanbase is large enough to warrant upgrading Isaac, he will. However, these other factors also need to be taken into consideration. I think we have a good chance, but these things will help us out a ton.