Okay so my speculation about the Square debacle.
The trio I believe (have in mind I have big bias for SNES era Square) is Geno/Crono/Sora, with Sora being the cut one.
I believe it in the scenario of Nintendo starting the DLC talk with SE a long time ago, like the Sora Yes tweet and the start SE dlc rumors ago.
I see Nintendo choosing characters who have big relevancy to their systems and not others. Sephiroth would be cut from talk here, since he is heavily linked to FF7, a PS1 title that represented SE changing from Nintendo to Sony. Cloud gets a pass because he is an icon of the franchise. (also, as a persona opinion, I think Sakurai wouldnt double down on an already represented 3rd party franchise when he has a chance to bring another one in)
I see Nintendo not choosing picks heavily preferred by one country with niche popularity in others. The 3 DQ (Slime, Luminary and Erdrick) would be cut here, since while DQ is really big in Japan, its niche in pretty much all other countries. (personal opinion, again, Sakurai has already expressed that he takes worldwide populairty in consideration, as show with Takamaru, but with the FE duo in Melee serving as an counter argument)
Nintendo would pick Crono for his popularity as a cult classic RPG heavily associated to the SNES.
Nintendo would pick Geno for the ease of his inclusion and as fairly requested character.
Nintendo would pick Sora for his popularity as a popular game and Disney character, since being associated with Disney brings populairty to him.
Talks for Sora would fall early because of Disney and for heavily promoting a game not announced fro release in Nintendo systems. (now this maybe reaching, but I'd like to also theorize with the Sora tweet from long ago. When being questioned about Sora being in Smash, a SE representative said "YES", with the tweet being deleted shortly after because it hinted at private negotions currently in the works)
With the remaining being Geno and Crono, two characters heavily associated with Nintendo with a following, the decision probaly was made by Sakurai or by Nintendo higher ups.
If anyone has any opinions about my theory on the talks, please reply. The discussions on this thread were a bit uninteresting for me until the developments in the SE case, so I'd enjoy to go further into this.