Personal thoughts on the pokemon roster:
Pikachu - Already confirmed. Important to smash and pokemon. He'll never leave the smash series
Jigglypuff - I wish she was cut (Most people I know that like her, only like her because of her mechanics in game, not the character itself), but she's a vet from 64 so that won't happen.
Unconfirmed vets
Mewtwo - A couple new movies, and megaevolutions, and a small scene at the end of pokemon origins. I had fun using Mewtwo, even if I had more problems using him than many other characters. He's the focus of the first pokemon movie, and is supposed to be the strongest pokemon. In short - Important to the series, popular, and has some reasons to come back. So pretty good chances.
Lucario - A very popular pokemon, and he had a movie. I would have thought he would have no chance. However, He's the first Mega-evolution pokemon you get in Pokemon X+Y, giving you a tutorial through a duel between mega lucarios, and he has a statue of mega-lucario in the mega-evolution tower as well. In short - His chances of returning are pretty strong due to his popularity, and still being relevant. I expect to see him in Smash 4
Pokemon Trainer - Charizard definently has a chance to come back because of mega-evolutions, being in pokemon origins, and in general being rather important to the series. Ivysaur doesn't seem to be important to the series at all, but bulbasaur and venusaur are talked about a lot. Swap out ivysaur for bulbasaur or venusaur. I don't care if there's no middle evolutions, none of the gen 1 middle evolutions were ever memorable/popular or important from what I've seen. Squirtle is rather popular, though his popularity seems to be tied with Blastoise. I'd be okay if Squirtle+ivysaur were removed and Charizard became his own character. If Squirtle returns, I want him to have his awesome shades from when he was in the Squirtle squad.
In short - Pokemon trainer might not make it back because of how much work he is. However, if they just have Charizard, I would imagine he'd have a much better chance of returning (only problem with that is that it's representing Charizard, not Red)
Pichu - I was surprised when this pokemon was added because no one ever talked about it before the game. Even after, I've only heard about Pichu because of people who played Smash. I can't see the popularity being there, I never saw any significance to the series other than that it's the pre-evolved form of pikachu, which we already have in the game. I don't see Pichu ever coming back, and I hope it stays that way.
Newcomers
In general - I find it unlikely to get anymore newcomers for the pokemon series. The Pokemon we have in the roster already is pretty good at representing the pokemon series already.
Meowth - He was planned for 64 smash, but since Jigglypuff and Pikachu is there, I think his time to shine is over even if he is more important than Jigglypuff to the anime.
Genesect - It's pretty popular, and has a new movie. However, I don't really see this pokemon being significat to the series later on, so I don't see it staying around. Maybe assist trophy or something?
Zoroark - Popular pokemon, it has a movie, and is one of N's more notable pokemon (and whenever people talk about B/W they always talk about how awesome N is). I'm a little worried about it's relevance to the series though, so I don't think it has a good chance of getting in because at this point it's going off popularity alone. It's one of my top 7 favorite pokemon (couldn't narrow it down to 6), others being Charizard, Scyther, Absol, Lucario, and haxorus, you can probably guess the one from the Kalos region. Of course, those other favorites don't have even a slight chance of making it in, but I'm more than happy enough that 2 of my favorites are in Smash.
New Pokemon Trainer - I would suggest Hoenn or Unova. Blaziken and Grovyle are popular, and thanks to the internet, Mudkips are too. Unova starters are liked by quite a few people, and are in quite a few spin-off games as well. No one ever talks about Johto starters anymore, and I've always heard bad things about the Sinnoh starters. As for Kalos, Chespin and his evolutions are either loved or hated, Fennekin seems to be the most popular. Froakie seems loved for his evolutions.
As for importance to the series, only the original can really be truly important since the later ones will be replaced eventually. This is why I find it unlikely to see a new pokemon trainer unless they were to release 1 trainer per generation, which I don't see happening at all.
Suggested Trainer combos
Johto - Cyndaquil, Bayleef, Feraligator
Hoenn - Mudkip, Grovyle, Blaziken
Sinnoh - Piplup, Monferno, Tortilla
Unova - Snivy, Dewott, Emboar
Kalos - Fennekin, Chespin, Greninja
Darkrai - Quite a few people loved the heck out of this character when the movie was out, and he's the main "villain" of a few spin-off games. While he's one of the 2 favorite legendaries (other being Rayquaza.... when Rayquaza's model doesn't look stupid), I really don't see him getting in the game.
Eevee - Popular pokemon. Apparently it was popular enough back in the day to make a whole sub-genre to the pokemon "fandom". It shows off the different types of pokemon as well, which is an important part of the pokemon gameplay. With that said, I don't think it'll get in at all.
Did I forget to mention any pokemon? I just glanced through the thread looking at all the pokemon.