I have a very hard time seeing a situation that isn't Brawl + Mewtwo.
Pikachu is obvious.
Pokémon Trainer I don't see getting cut or replaced. He is an incredibly iconic part of the franchise and Red is the most well-known variation of the character. Plus going through the effort of replacing three characters with another three character is more work than I see Sakurai doing.
Jigglypuff would have been gone by now if he was going to be cut. The fact that he's been kept in 64, Melee and Brawl shows that Sakurai has enough interest in keeping her around and I do think that he'll be prioritized to where he comes back.
Mewtwo is the closest thing to a lock at the moment. Mewtwo is likely the most wanted character period (only Mega Man can dare to compete with Mewtwo in popularity), was planned for all three games and is being heavily promoted by the Pokémon Company. I don't see any reason why Mewtwo would be left out and at this rate, it's a matter of how Mewtwo will return.
Lucario I have a very hard time seeing going. He's also been heavily promoted as of late and has remained very popular along with having importance in the franchise thanks to being the definitive Gen 4 mascot. If anyone were to be cut, it'd be him, but I really don't see cuts happening to this franchise, especially with Sakurai planning seven, if not eight characters (transformation included).
The issue with other Pokémons is that it's simply unlikely that Sakurai would go for one nor do I see the Pokémon Company pushing for a newcomer (not counting Mewtwo's new form). Zoroark's heyday is gone, Genesect probably won't get in based off the movie alone and Victini really missed its chance. The only possibilities at the moment are Pichu and maybe Plusle & Minun (and that's only if they were planned, otherwise their chance are good as dead) and even with Pichu, I don't see him coming back unless DLC characters come back. It's a shame about Deoxys because it truly does deserve a spot in Smash.