That's now though. You're forgetting that we've already had 2 massive fan requested characters in K. Rool and Ridley and you have to remember that there's more than just the die-hard Smash community to cater to. Furthermore that we've probably got at MOST 4 unique newcomers left on the base game (possibly 3).
We're going to have a new Pokemon for sure. Geno seems like a certainty due to his path into Smash and Sakurai being a massive fan. That's already 2.
What seems more likely for the last 1 or 2 newcomers. A Zelda newcomer, a 3rd Party newcomer, or an obscure GBA RPG sword fighter who was so irrelevant that last game their sole piece of content was removed?
I will grant you that if there are more newcomers than I'm anticipating that Isaac has a much better chance though.
There were still two songs present (one of which was new) even with Isaac's AT gone. Speaking of which, we don't know
why the AT was removed. Sakurai has never spoken about it. But if it were because of "obscurity", then why are Starfy, the Infantry & Tanks, and Saki all still around? Why would they add ATs like Takamaru or Sable? The former of which Sakurai noted specifically wasn't playable
because of his obscurity to western audiences.
It's possible that Isaac's AT was simply cut because of 3DS hardware limitations, or they might've even had plans to make a Golden Sun character playable since Dark Dawn hadn't quite become irrelevant yet (Shulk's game was actually older, mind you). We don't know.
Beyond all else, if Sakurai says he's taking from the ballot, then that's why Isaac will get in. We don't have any reason to believe he's going to be given lower priority simply because his game is not as well-known as Skull Kid's, for example. Obscurity isn't as big of a stickler as it was back in Smash 4. Otherwise, the only reason we'd ever consider
Geno plausible is Sakurai's own love for the character. Right now, signs are pointing to this game being about what the
fans want, and if the fans want Isaac, Sakurai will give it to them. Isn't that the same reason why Banjo & Kazooie would get in?
Isaac isn't assured, but don't count him out even if there
are only four characters left.