Strictly looking at 3rd Party Characters that people really seem to want, I think Shantae is in pretty good spot - most of the other Third Party characters just have a ton of obstacles in their path.
Banjo-Kazooie are owned by Microsoft. While that doesn't knock them out immediately, I have a really, REALLY hard time imagining Nintendo paying and sharing Money for the DLC to/with one of their biggest rivals in the console market. I just can't see it happening, unless MS does allow Rare to make a Banjogame on 3DS or some other exclusive stuff, but that doesn't seem to likely either.
Snake - Kojima and Konami are on bad Terms right now. Seeing how Snake was only in Brawl because Kojima and Sakurai are buddies, I'm not sure if Sakurai wants to support the Company that basically kicked his friend out and removed his Name of all the boxes of the games he made. Nintendo probably has the last word, so when they say Sakurai has to, I guess he has no choice, but yeah, I'm not so sure about him either.
Bayonetta is too sexy. Yeah. Kind of ironic to say it, as this is being held against Shantae permanently, huh?
Bayonetta is just completely built around her sexyness. She freaking STRIPS in her games. I simply can't see her fit in without heavily bumping up the Age Rating. Some might say "Well, don't strip her then", but Sakurai likes to do rather faithful interpretations of a character (when he doesn't include them very last Minute, that is), so stripping (hah) her character of the things that defy her just to make her fit into Smash doesn't seem like something he would want to do - it would be like adding Pikachu to the roster and giving him no electric attacks.
Then there's also characters like
Rayman (a fav of mine) - he's pretty dang popular over here, but he doesn't seem to be too popular in Japan. What worries me about him isn't the lack of popularity in Japan, but the popularity combined with the cost that Ubisoft might charge for Nintendo to use him. Maybe they want a lot of Money for him and it isn't profitable enough when a whole Region doens't really care much for him? That's a HUGE speculation though, I think he has a good change of getting in.
And then there's the two Shs, the Indie characters:
Shovel Knight and our beloved
Shantae. I think both of them have a good shot. Shovel Knight was INSANELY popular early in the Ballot, so if they did some early picks, he has pretty dang high Chance of getting in, even though his lack of a japanese presence and him losing a lot of steam towards the end. Shantae on the other Hand started off slowly and gathered a ton of steam towards the end. I think Shantae has a Advantage, though: Japanase Appeal. I wouldn't go as far and say that she has a big fanbase in Japan - she really doesn't - but the fact that her games have only been quietly released via Steam so far and her still having even some high profile japanese fans speaks volumes. Now that her games are getting released in Japan, I can see her getting really, really popular (heck, she's already picking up!). Maybe Sakurai saw how beloved she is over here, recognized her appeal to japanese People and said "Yep, I think they'll like her, let's put her in!" But even if the Smash 4 DLC gets released and she's not one of the chosen characters, I can see her getting so much popularity that she'd be an insanely high contender for Smash 5. A Bonus for her and Shovel Knight are also the fact that Wayforward and Yacht Club probably won't ask for much Money to get their characters into Smash (if at all), since it gives them a lot of exposure, so that is probably a plus and does reduce the risk of losing money in case Japan really does not care much for them (which I don't think is the case anyway)
But yeah, just my two cents. I think Shantae has a good shot of getting in third party wise, but there are quite a few Nintendocharacters that are even bigger possible "threats". Heck, maybe we won't even get a single 3rd Party Character! But yeah, we'll see what happens. :D