This may seem naive, but I really do think the 3rd party characters that share a company are tied together at this point.
Package deals, if you will.
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Granted, I could be completely wrong, but unless the roster sees some massive downsizing (I think a lot of characters will go before third parties) or the director just doesn't want a character anymore (maybe that's what happened with Snake?), I can't see any real reason we'd get one but not the other.
Personally, I think the companies with only one character are more likely to leave and one of them ain't going anywhere.
Sega and Capcom are tied pretty closely now with Smash. They have a lot of content in the game from characters, to stages, to costumes, etc. Namco is in deep as well (heck they made the game). I think all three companies have seen just what Smash can do and trust it fully.
Square Enix is the wild card here. They jumped on late, but they jumped on. For someone as protective with their properties as they are, that says how much they trust Sakurai and the Smash Bros IP. I think the only thing that would affect Cloud coming back would be the director. I'm not sure if Cloud will stay or go, but I'd love to see him return personally.
Konami? I've given up predicting what they're gonna do. Snake. I love ya bud. I want ya back, but you're in a strange place right now.
Might as well say some things about new third party characters since I'm here.
Yeah, I think Capcom, Sega, Namco and Square could get more characters. It wouldn't surprise me if another Sonic character came in and I think Namco getting a second series represented is rather likely. I'm personally betting on Sakurai revisiting his Heihachi idea. Konami is Konami man....
I think next Smash could see the introduction of a western third party. With Nintendo going out of their way to get games like Skyrim, Fifa and 2K, as well as working directly with Capcom with their hardware, I think they're becoming rather serious with their third party support. I don't see Sakurai choosing one unless they did well on the ballot, but I could see Nintendo's new management pushing one real hard. I don't know who that would be though...
An Ubisoft character like Rayman? Ezio?
A Bethsheda character like the Dragonborn? Doomguy?
An EA character like.... uh.... well damn...
Point is, I think western third parties are in the running now, which I couldn't say for Smash 4.
I also think smaller third party series have a shot as well. This not only applies to popular indie games like Shantae and Shovel Knight, but also games from more modest non indie studios like Grasshopper Entertainment. Yes I think Travis has a shot now. Especially if No More Heroes 3 becomes popular.
I think Bayonetta opened the doors for third parties. Yes, as the ballot winner, she is a bit of a special case and she is tied directly to Sega, one of Nintendo's closest partners, but I feel that she gives precedent to the idea that third party choices don't have to get in on their legacy (
not that these guys did necessarily, but it certainly helped). Sakurai is willing to include more minor third parties if he feels its what the fans want and if they can provide a fun and interesting playstyle.
Guests need to be fun above all else after all.