None of the third party costumes have returned in base game, even the ones that had spirits like Megaman X or Zero. It's probably just that they wanna resell the outfits and need to spread out the releases.Why? Monster Hunter is literally represented in the game already and the other Capcom costumes got brought back, why not the 2 Monster Hunter costumes?
I don't get Geno either since he also has a spirit in the game so there's no reason his costume wouldn't be back, but atleast with him you can make the "Square is weird and so is Geno so his costume being gone doesn't mean anything" argument, no matter how much I disagree with it.
I can also totally see Geno being upgraded to a premium Mii outfit considering that Nintendo has taken down two Super Mario RPG tracks from Youtube a couple of months ago, similar to what happened with Sans.