Nintendo and Squeenix may have been on better terms in the past...but then why Sora? Even IF there was representation from them, Sora is one of the least possible choices (slightly ahead of, say, Palom and Porom). A BIG part of the Smash line is the history of Nintendo. Hence, the trophies, the inclusion of old franchises that have little chance of remake, heck, the characters in general. All point to the universes of Nintendo.
Sora has NO impact whatsoever on any of this.
The ONLY thing that Sora has going for him is "he's popular." If that were a valid reason, then he still wouldn't because Master Chief is way more popular than Sora is. And Cloud/FF7 characters more still.
What has Sora done for Nintendo? What has he done for video games? His only purpose is to serve as a generic connection in what is essentially an official Disney doujin game. And oh my, how generic! Ridiculous spiky hair, poofy pants, fights with what is essentially a spiffy-looking sword...At least when Cloud did it, it wasn't stereotyped just yet.
If we wanted a generic character from Square/Enix, how about something that actually stems from the series with a Nintendo history?
No Sora. Please, no Sora.