If the game is a remake, it'd be because Nintendo doesn't usually roll out the red carpet for them as much as they do new titles. I mean remakes and remasters almost never affect the Smash roster.
If it's a new game the chances are better, though the chances of it being a new game are smaller. That said, it's also entirely possible they wouldn't intend to intertwine the game with Smash-related promotion just because that's an uncommon occurrence. I mean Nintendo opting to push a character through Smash is irregular enough that it not happening to a series that it's never before happened to would not be weird. It actually would be the status quo.
I can see both sides of the argument really. You're right that there isn't really a reason to think anything special would happen for Isaac if it was a Golden Sun remake since they don't usually affect the Smash roster....
but on the other hand I can't think of a remake in recent memory that even had a character that was even remotely likely or popular as a possible addition. There's been a stream of Mario and Zelda remakes (along with the Metroid one and also various Pokemon ones) that I can't imagine how they would have had an affect on the Smash roster anyway.
In terms of remakes it may just be the case that there's never been a significant character from those remakes that would warrant their addition to the roster.
I do think a Golden Sun remake would be fairly unique in the sense that:
1. The reason for it existing in the first place could be because of the ballot vote and Isaac's popularity. So it's potentially already tied to Smash Bros through that.
2. It's the only remake I can think of that actually has a prominent character (the protagonist) attached to it who is not already on the Smash roster and already has significant fan demand behind them.
So I do agree with you but I also think there could be reason to believe that a Golden Sun remake could be a unique situation.
I think if they had decided to revive Golden Sun because of Isaac's Smash popularity it'd be crazy, even contradictory not to include some Smash promotion of it.
I'm not sure if I'd go as far as to say it was contradictory.....because it's not like it was Sakurai who decided to work on remaking Golden Sun.
but I'd be very surprised if a Golden Sun remake became a reality because of the Smash ballot and then Sakurai just didn't even consider adding Isaac to the roster even with that knowledge.