Somewhat hot take, given it goes against the general opinion of the thread, but I think Geno's Mii Costume being missing makes me think he's in.
Geno's Mii costume wasn't just any Mii costume, it was one that had a lot of fanfare surrounding it. Rather than throwing it in montage as is standard practice, Sakurai slowed the direct down to show it off and give it a fighter-style splash screen. It's clear that Sakurai really liked having Geno's costume in the game, so its absence is pretty surprising.
Now, I have seen a lot of people throw Geno's costume returning with a remix and possibly a redesign, but that really leads into my second point: Why didn't that happen with Hero? In Smash for Wii U/3DS, Geno released specifically alongside Cloud to make things thematically work as a Square-Enix package, so why wouldn't they do that again? I doubt it's due to licensing issues, considering Geno and Mallow had base game spirits. I suppose they could be saving it for another Square character like Sora or 2B, but why they would wait to get it out to market?
I have similar feelings about the absence of Heihachi's Mii Costume: high fanfare for a Mii Costume upon announcement, an obvious spot to put him was missed with Terry's wave, and the general lack of Namco spirits makes me think they're being saved for his release.
Now, I have been wrong on these types of things before, so take it with a grain of salt and all that. However, this is genuinely what I think.