The problem with SE is there are no characters that separate themselves from the pack. People end up getting stuck asking for a token SquareEnix character as though there is some quota to fill, where as with Sonic the Hedgehog and Megaman it was clear they were wanted. Had nothing to do with Capcom or Sega, just the characters. You can't really say that with SquareEnix, not without going down some sort of list. The only character even remotely close to that is Geno, but he wound up being the result of a cultish fad than anything else. Unless there is a Solid Snake situation where other reasons besides popularity are in play I can see a character happening, but beyond such an anomalie I don't see Sakurai going out of his way to include anyone like he did with Sonic the Hedgehog and Megaman.
Geno's only hope really comes from his pre-Brawl popularity (could argue how he's an easy fit in comparison to other third-parties, but it doesn't matter that much) and it's a very, very small hope at this point considering Sakurai going to be dealing with the painful process of successfully fitting in two, three or maybe even
four third-parties this game. Geno also suffers from being such a minor character in both the Mario universe and within Square Enix and much more well-known competition from Square Enix. I don't think Sakurai would go through the trouble to include him.
There is only one character left that could hope to obtain the massive demand that got Sonic and Mega Man in and that is Cloud (not just from Square Enix, but third-parties in general). Cloud's potential for popularity would certainly be much bigger than that of Mega Man although likely not to the same extent of that of Sonic. What's keeping him from reaching that is how associated he is with Sony and I'd wager that a big reason why quite a few people rejected Snake was because of him being so relatively associated with non-Nintendo platforms. What Cloud needs in order to be incredibly popular for Smash is a FFVII remake on a Nintendo platform and let's be honest here, chances are it's not coming to a Nintendo platform. So while it could happen, I don't think Cloud will ever get the sparks necessary to be a heavily demanded character. Not that being generally associated with Sony directly hurts a character's chances, but it does keep Cloud from being highly wanted.
I honestly think this will be the last time we see third-parties in a Smash game. No one will ever prove to shock the audience as much as Snake did, no one (outside of perhaps Cloud) will ever be massively requested to get in like Sonic and Mega Man and there is no one that will ever be as iconic as Pac-Man. Smash 5 (should be there one) will likely be only Nintendo characters again.
