While I do think that the other two have a greater chance of being included, I also think that Sceptile would be the best choice for a Pokemon newcomer (should we get a second one).
When picking a newcomer, recency plays an important factor. Who would care for a random first generation Pokemon if they opted to include one all of the sudden? With Pokemon, no one of them is really more important than any other (except for Pikachu maybe, but he is already in the game). A newcomer from the sixth generation would therefore make the most sense.
Greninja is proof for this, as he was choosen simply as a rep for X & Y, and not because he is popular since we know that he was choosen long before the games came out. So should we get another Pokemon newcomer (which I don't really think will happen) it would most likely either be another Pokemon from X & Y or one that represents OR & AS.
Now most people would say that Sceptile has no chance, simply because the remakes aren't even out yet. However, for Sceptile to be chosen the games wouldn't need to be finished, as is proven by Greninja. In fact, as long as Nintendo/Gamefreak had the idea for making remakes of Hoenn before the Smash 4 roster was decided he would still have a shot since. Since the original games have been out for years Sakurai wouldn't have to wait for Gamefreak to finish the character first, and even if he did have to, that didn't stop him with Greninja.
The only remaining question would be: why him? Wynaut any of the other Hoenn Pokemon? To cut it short: besides legendaries, the starter Pokemon are always among the most popular Pokemon from their respective generations (they are the first Pokemon you get after all). Swampert would be hard to implement due to being quadrupedal (not impossible, but it definately hinders his chances). Blaziken on the other hand would be easy to translate into Smash Bros and is also really popular. However, while there is no rule for there to be starters of all three types like many already have pointed out, one thing that would helpt Sceptile to get in over Blaziken is his potential to be more unique. Blaziken is Fire/Fighting, and we already have Pokemon of both of these types in Smash, but we don't have any Grass Pokemon yet, which could set Sceptile apart from the others.
Again, I don't actually belive that we will get him. It would be possible, since even with Mewtwo, Jigglypuff and Sceptile we would only sit at seven Pokemon characters, which is only one more than we had in Brawl, and since Fire Emblem also got two new characters (although one is a clone), but I don't belive it is very likely. Sakurai simply might not feel the need to add another Pokemon, and even if he did, with 719 possible choices, there is no guarantee that Sceptile is even on his radar.
On a side note, I do think we will get Jigglypuff back, and Mewtwo has a decent chance as well, though I don't think he is as certain as some people say.