I would argue the opposite, actually. From a business perspective, they want to make DLC characters who people will buy. The question is really who would make more money for Nintendo/Square. If it was Sora, it'd be split between three companies instead of just two. And Geno 100% would sell as much as Sora. I'm not going to say one would sell more than the other, because I can't say who would, but for Sora to make more money, he'd have to be 1.3 times as popular. In general? Yes, Sora is probably way more than 1.3x as popular as Geno. Among people who are huge fans of smash bros? People who are going to buy dlc for this game? Geno is almost certainly just as popular if not slightly more. Maybe slightly less, too. Again, I have no idea. If Nintendo really cared about promoting games as much as you're saying, they wouldn't have added Joker. A character from a game not on a Nintendo console.
Also, every single mario RPG (paper/&luigi/etc) borrows and is inspired by SMRPG heavily. Bowser's entire personality in these games is practically the exact same. Meaning, Geno doesn't just rep one game, he, in spirit, represents an entire sub-series of mario, that being the RPG games. Not to mention the chance of a sequel/remake for switch.
Even if Nintendo decided "from this point on, after Joker, only characters that advertise games for Switch," they wouldn't put in Sora. He's gonna be on playstation forever. Yeah, there's a chance KH3 will be ported to Switch, but there's also a chance of SMRPG 2, or SMRPG HD.
Sora and Geno are easily the two best choices for DLC, and if ownership of characters and such weren't complicated, they'd be equally likely. It's just that Sora is partially owned by Disney, and Sakurai likes Geno more (as far as we know) that makes Geno seem more likely to me. Apparently nobody has ever said no to Nintendo for smash, so Sora isn't totally out of the question because of Disney, obviously. I just think Geno is slightly higher. Especially because he's got more fan demand since Melee.
Also for the record... KH2 is probably my 2nd or 3rd favorite RPG of all time, and Sora would make me very happy if he got in. I have nothing against the dude. I just wish KH3 were coming to switch so I could play it