Snake
Chance- 60%
Here are the facts:
-For Brawl, Sakurai worked hard to create an original move set for Snake. Snake ended up being one of the most unique characters in any fighting game ever, and it's not like Sakurai to just throw away a fighter that brings so much to the table. Not to mention that Sakurai is clearly a big fan of the series, and tweeted pictures from the 25th anniversary celebration, which occurred right around the time development began on Smash 4. If Snake isn't in Smash 4, Sakurai isn't why.
-Kojima "begged" for Snake to be in Smash going all the way back to Melee. Kojima has also made a public request for Sakurai to include Snake in Smash 4 as well. If Snake isn't in Smash 4, Kojima isn't why.
-Development on Smash 4 started in around March of 2012, right after the release of Kid Icarus: Uprising. Metal Gear Solid: Snake Eater 3D released in North America in February 2012 and worldwide in early March. This means that when the roster list was being put together, a heavily promoted Metal Gear title developed by Kojima himself had literally just been released on a Nintendo console. It's worth noting that this was just over two years ago, meaning Metal Gear has had a title released on a Nintendo console more recently than Mega Man, Metroid, Star Fox, F-Zero, and Mother. If Snake isn't in Smash 4, "relevance to Nintendo" isn't why.
-Metal Gear is a series with a very goofy, over the top, hyper-real aesthetic. Snake is not a "realistic" character, as is clear to anyone who has actually played his games. One of the bosses in Snake Eater is a man made of bees, for instance. This bee man was supposedly instrumental in defeating the Nazis in WWII. It's all very silly. The games are somewhat violent and tackle some weighty themes, but the same could be said for Metroid, which has a much darker and more serious tone in general than Metal Gear, discounting maybe MGSV, which isn't even out yet. I would argue that the only reason Metroid games have never been rated M is because the violence in those games is directed towards aliens instead of human beings. Snake is no more out of place among Mario and Link than Samus is. And regardless, this is a crossover fighting game, so everyone is a bit out of place, that's the point. Snake is an important and beloved video game character, and while he's not quite as iconic as Mario or Pac-Man, he can certainly stand shoulder to shoulder with Sonic and Mega Man. Snake may be more associated with Sony than Nintendo, but this argument would only hold weight if he wasn't already a veteran. If Snake isn't in Smash 4, "not fitting in" isn't why.
-Over the past few years, Konami has demonstrated a pretty disrespectful attitude towards most of their IPs outside Metal Gear, often failing to give them any significant promotion. This paints a picture of a company being run by people who don't really "get it". Konami has also yet to support the Wii U, with one marketing rep making openly hostile comments towards it on Twitter. While Konami has a long a distinguished history both with video games in general and with Nintendo, the company, like Capcom, is undergoing a bit of an identity crisis and is quite possibly being run by idiots. If Snake isn't in Smash 4, it's because of Konami.
-At the moment, the only concrete evidence that Snake isn't returning is that he hasn't been announced yet. Kojima did not say that Snake isn't in the game, only that he doesn't know, but "doesn't think so", and with a big smile on his face at that. I would say that if we haven't gotten a confirmation of Snake by the end of August, then he's out, but until then, his chances are just as good as any other veteran besides Ivysaur and Squirtle, who are definitely gone.
Want- 100%
Brawl was my gateway into the Metal Gear series, which is now my favorite video game series of all time. Did you hear that Konami? Snake appearing in Smash Bros led directly to me spending numerous amounts of money on your silly stealth games, including buying a version of Snake Eater no less than 3 separate times! Snake is also my second favorite character to use in Brawl (after Olimar). I really, really want him back in. Now that Tingle and Waluigi are disconfirmed (I know, I know), Snake is by far my most wanted character. I honestly don't understand why he's so widely disliked. Play his games and you'll see that regardless of what console they appeared on, it's an absolutely wonderful and hugely influential series that deserved its representation in Brawl and deserves representation in Smash 4.
Isaac
Chance- 35%
I have much less to say about Isaac than Snake. Basically it comes down to this: it's either him or Shulk. Both are blond male JRPG protagonists, both will elicit a "who?" from the general public at large, and both are sword fighters with magic abilities. I know this is far from an original conclusion, but I think Chrom's disconfirmation has proven that Sakurai does not like redundancy in the roster. Right now, it's looking like Shulk is more likely, given X's upcoming release, Monolith Soft's obsession with retweeting Sakurai, and the Gematsu leak, which I sort of still believe.
Want- 70%
I have not played Xenoblade or the Golden Sun games, but I definitely want Isaac more than Shulk. Isaac, aesthetically, has much more going for him. It may be difficult for people who have played and fallen and love with Xenoblade to appreciate this, but Shulk is literally the most generic looking jrpg protagonist possible. Isaac has his own identity and just looks more like a Nintendo character. In addition, Isaac has telekinesis and rock magic, while all Shulk has is a sword that can predict the future or something. Isaac sounds like much more fun to play as in Smash. Just the "push" attack that he had as an assist trophy alone would make for an awesome and unique special. Unfortunately, it looks like they're going with Shulk, but I'm personally still holding out hope that we get Isaac instead. I think the fact that we still haven't seen his assist trophy is either a great sign or simply means he's not appearing at all.
Predictions
Dr. Mario- 1%
He's going to be a costume.
Bowser Jr.- 5%
I never understood the enthusiasm for this character in the first place, but regardless, I seriously doubt we're getting another Mario newcomer, and if we do, it had better be Captain Toad.