Isaac has always been an oddity for the smash speculation scene. Realistically speaking, there has never been anything holding him back when you compare him and his series to all of the other characters that have become playable in the games. Especially the first party ones. That's another reason we want to see him here because it's the only way we will every have finality to all of this. Sakurai has never talked about Golden Sun or Isaac so we've always been driving blindly, and that's the only reason we can even presume that he's not been playable. Not that Sakurai hates GS or anything; that would be foolish. Just that when he gets to decide the roster, he passes over GS for some criteria that doesn't make sense from what we see.
I think even to this day the people that write him off don't even realize that's he's 1st party Nintendo. He sticks out like a sore thumb. It's hard to let go of that feeling of righteous indignation about the whole thing.
After reading a past interview from Sakurai regarding some of the Smash 4 newcomers, he mentions that MegaMan and Villager typically wouldn't be the types of characters in a smash game because of their gimmicks in their movesets (and I'm sure this would apply to Shulk as well).
So that tells me that Isaac was a no go for Brawl from the get go, Isaac would definitely be the very definition of a gimmick character if Sakurai was incorporating djinns and magic/utility psynergies.
Skip to Smash 4, where there were two games being developed at the same time, one a handheld. The 3ds took priority over character reps. Two time vet Ice Climbers got cut for not working on the 3ds. Pokemon Trainers gimmick was done with altogether, Lucas got on the chopping block cause his final smash was causing problems etc. If we assume Isaac got cut for similar reasons regarding the 3ds, no sense in putting work into Isaac if he was only going to work on one system anyways, like with Ice Climbers.
That coupled with Smash 4's newcomers being more promo heavy than normal. I'm pretty sure Isaac's competition was Shulk, both blonde hair, blue eyes jrpg protags with their last game released in the same year. But they chose to go with making Xenoblade into a mainstay series, X released a year after Smash 4 and the new 3ds version of Chronicles released again. Jumping straight into Golden Sun 4, a continuation of a previous story may have been considered more of a hard sell than starting with a fresh cast of characters with their own story. Of course this goes without saying, Shulk's gimmick worked on both versions, Isaac's hypothetical moveset gimmick didn't. So of course if Shulk was chosen, his series gets to continue to live.
Though now, nothing should be holding Isaac back aside from Sakurai himself finding him unrealizable or something. There's only been one new first party franchise (Inklings) no newcomer so far has a crazy gimmick movesets (like how Sakurai said Palutena was one of the hardest characters to make with all her customs and while a vet, it was stated Lucario took a while year to create cause of his aura mechanic).
No matter how you slice it, Golden Sun is one of Nintendo's notable big franchises still unrepped, Isaac is one of the most popular first party requests still not in, his popularity has stood the test of time despite his assist getting cut in 4 and the last Golden Sun game going on eight years now. Sakurai's using the fan ballot, a lot of heavily requested characters are already in. Isaac literally has one foot in the door already with his assist model to work off of and please can we be spared from the impending you know what storm upon Isaac's deconfirmation, let Ultimate finally be Isaac's game.
