If I had the chance to put in a Third Party Character that was from one of Square's games, it wouldn't be the wood puppet and cloud with arms. Instead it would be significant character from Square's library and I imagine that's what everyone thoughts would be between Bandai Namco/Nintendo/Sora Company when they begin and end dealings with Square for licensing agreements.
You have more chance of Sora from KH being a character than Geno. If I remember, I think Disney has already given the Green Light at one point as long as it's faithful (Which it will be with vast past evidence up to this supporting this point) and it's all up to Nomura to decide if he wants to (Sakarai and Nomura have actually been interacting a lot more since the Cloud Update so if he was going to be in, it would be before Sakurai stops with Smash Bros all together.) So why waste negotiation time, dev time and money having a niche character when there are far more known, more influential and well liked characters that are better to be in it.
I don't think people realise that Sakurai is one of the main reasons why so many beloved characters from third parties make it in, man has tons of connections and is respected by everyone for it. The time that Sakurai retires from Smash could possibly mean losing some third party characters to be licensed for the next Smash Game as Sakurai was always the one managing to get it going because of third parties trust in him. (Along with support from Nintendo and Bandai Namco of course.)
If another Smash game does get in and Sakurai leaves. I can imagine Cloud and if it happens for Ultimate, Sora not being in the next one. SNK, Sega, Platinum Games, Atlus, Capcom, Bandai Namco, Toby Fox, Studio MDHR, Koei Tecmo, would no doubt have their characters back in if asked to. Microsoft would no doubt be fine as long as relations are still fine, interactive and not soured (And with Zenimax/Bethesda now owned by Microsoft, any past deals with Bethesda is done by Microsoft now and Microsoft have stated they will keep previous dealings, licensing and negotiations that were done before Microsoft acquired Bethesda which would make negotiations and dealings more easier for both parties.
Konami have gotten better with licensing than before as even if they don't bother making games anymore for their main franchises, they know they can still earn some bucks from licensing to third parties so likely possible for Castlevania and Metal Gear to come back. Square is a tricky one as it depends on which franchise that the Sora Company/Nintendo want represented. Any Square franchise that isn't involved with notably known companies or people who are very strict with their licensing has far more chance appearing than Chrono Trigger, Kingdom Hearts or anything done by Nomura or the Final Fantasy Composers). There are other companies involved but Smash has so many involved now (With Mii-Fighters costumes and Spirits) that it's hard to remember all of them from the get go so I might of left some obvious ones.
But as for potential character picks. Sakaurai wants Characters not only well beloved and fun potential for Smash but ones that also influenced the gaming industry today, most of the character choices are from Nintendo with Sakurai only choosing a couple like SNK.
In terms of those fields filled. Doom has influenced gaming so much in not only the First Person genre but the eventual evolution into 3D gaming as well so Doomguy is a good choice on that alone, plus with Nintendo/Sora already done dealings with Bethesda and Microsoft before Bethesda became owned by Microsoft, I don't think getting permission and licensing is going to be hard to do so. Plus you be surprised how Doom is popular in Japanese Media even with the violent content making CERO sweat as there are many homages for the Series alone. The only problem with Doomguy is naturally is the content he represents but they did well with Bayonetta and Joker so I doubt it will be a problem.
Crash could make it in but Activision is kind of weird and strict on it's dealings so I'm up in the air for that one. Makes sense from a Gameplay and influential history too (Plus Crash was actually somewhat popular in Japan and him being changed style wise for Japan alone for so many years could make it seen as a alt skin of sorts.)
I don't think we have had another Bandai Namco character aside from Pac-Man yet so I could also see a Tekken/Soulcalibur character pop up and if it were, my main guess would be Yoshimitsu to hit two birds with one stone essentially to represent both franchises. Legacy wise is obvious, Yoshimitsu would work game play wise for all the crazy stuff he can pull out and Nintendo outsources Smash to Bandai Namco for development and have always had good relations with one in other (Hell it's how we got Link in Soulcalibur 2 for Gamecube) Sakurai and Harada regularly talk with each other because of both being involved somewhat with the dev team for Bandi and we know they have interactive recently since Harada mention Sakurai in the Fighting Game online gathering of developers discussing online connectivity and Rollback and plus we had a Haihachi costume back in Smash 4, So yea I can also see any of the Tekken/Soulcalibur characters getting a representation of some kind in the future.
I really don't understand where all this shit about relevancy is coming from. Smash has proudly showcased irrelevant characters for years. Almost two decades, really. Ness is no more relevant than Mallow or Geno, he just has a more rabid western fanbase. Ice Climbers were featured in one game from the early NES library, and even then most players didn't see Nana if they only ever played single player. Duck Hunt was even more irrelevant given the age of their game (or games if you include the Wild Gunman Final Smash), which I don't think even existed on Virtual Console before becoming part of the roster. Sakurai would've included even more irrelevant characters if Nintendo had let him, like the girl from Famicom Detective Club. The thing that binds them all together is that they're all fondly remembered by the fans of their games, which is really the important thing.
The difference is though that Ness, Ice Climbers and Duck Hunt are owned by Nintendo making them first party characters and would have no problem getting in regardless of Fame or relevancy. Fuck, Mr Game & Watch is a perfect example of why this doesn't matter to Nintendo owned Characters and since the start of N64 & Melee they had characters that had games that never appeared in certain regions across the world (Earthbound never came out in Europe originally, Fire Emblem's Marth and Roy was never known outside of Japan).
