Cloud's the most popular, but if there's a FF rep, I SERIOUSLY doubt it'll be Cloud. Why? Because he's absolutely worthless to Nintendo.
Look at the 3rd party characters so far: Snake started on the NES and starred in two games there, and Kojima is good friends with Sakurai and Miyamoto. Sonic was Nintendo's only true rival for many, many years, and after a while, made his home primarily on Nintendo consoles. What did Cloud have? A cameo on a much-maligned spinoff of a series by TWO SEPARATE THIRD PARTIES.
Not to mention that despite the magic/materia/summons (Which aren't even Cloud's primary form of offense), at the end of the day, Cloud would just be another swordsman. And Nintendo has plenty of those to not blow a bunch of money on another one. I mean, three perfectly good characters were AT'd just because they couldn't offer anything new to the gameplay, and really, could Cloud?
Cloud being in the game would be the ultimate proof of Sakurai selling out.
Now, since Geno is probably not going to be counted as a Square rep if he makes it, AND the new "There's going to be more 3rd party characters" rumor, I'd say that a FF character isn't out of the question. I'm not terribly familiar with the SNES FF's (I grew up on the Genesis), so I'll let the rest of y'all decide who'd be the best bet. I'm just pretty sure that if we do see a FF character, it'll be one of the older guys. You know, ones that actually MEAN something to Nintendo.