I remember back in the K.Rool thread a lot of people were worried that unlike Ridley's, K.Rool's popularity had never been brought up in the past other than the Mii costume, and you see how that turned out. The fact Isaac hasn't been brought up isn't that much of a problem, and I think he's the kind of super popular character who, if he wasn't gonna be playable, would've been acknowledged already in some way. I am glad Sakurai at least disconfirmed Midna so early or I'd have been crushed when finding out the truth, and I am sure he's aware Isaac is too popular not to be on people's radar.
The only alternative I can think of is that Isaac isn't in the game in any way whatsoever, which seems unlikely given how all out on the fanservice Ultimate is. They even brought back Scizor and Gray Fox, which means bringing back assist characters isn't out of the question, so if he wasn't playable, he would've at least been made an Assist Trophy again.
That said, does anyone know if Golden Sun was, like, disproportionately popular in Europe or something? I am amazed that literally everyone I know with a GBA played Golden Sun(except me, i am ashamed), and knows Isaac and wants him in the game. He certainly doesn't feel like the niche character so many people claim he is.