I'll actually be very disappointed if we don't get either a second Pokemon Trainer or at the very least a replacement for the original. I know it's considered really assholish to want a character out, but having 5 out of 6 Pokemon reps be from the first game is just ridiculous, and it'd be even worse if Mewtwo was added back or Lucario was cut.
If nothing else, I'd like for Mewtwo to return and a second Pokemon Trainer to be added with three Pokemon from a different gen, just to even the scales a bit. It may be asking a lot, but I think Sakurai kind of worked himself into a corner there by adding so many damn Gen 1 Pokemon.
Red is the most iconic trainer, and the Bulbasaur, Charmander, and Squirtle lines are the most iconic starters. I'd hate to see them replaced with their less memorable counterparts just for the sake of generational diversity. The first generation is always going to be the most important. A Pokémon Origins TV special just recently aired, and even the X/Y games pay homage to Red/Blue with the Kanto starters and renewed focus on Mewtwo.
Jigglypuff's continued presence in these games makes it tough to lay out a truly appropriate Pokémon roster. She doesn't really "deserve" to be playable, but at the same time her absence would offend longtime fans of the series.
Pikachu should be in Smash Bros. no matter what. Nobody's going to argue with that. I also think it's important to keep the Pokémon Trainer (as he appeared in Brawl) since he's the protagonist of the actual video games. Mewtwo should also return; it's easily the most iconic legendary, it's rare in that it has a backstory, and as mentioned, it's still relevant.
Sakurai seems to favor the non-starting, non-legendary "promotional mascots" when choosing playable Pokémon from the additional generations. Generations two through five have each had one of these -- they tend to be the Pokémon who are revealed early on, are heavily merchandized, and appear in movies.
G/S - Pichu
R/S - Plusle & Minun
D/P - Lucario
B/W - Zoroark
My absolute pipe dream of a Pokémon roster would be:
Pikachu
Jigglypuff
Mewtwo
Pokémon Trainer
Plusle & Minun
Lucario
Zoroark
That's technically nine characters, which most people would say is too many, but considering Pokémon is Nintendo's second-biggest franchise I'd be completely fine with that. There are bound to be at least ten Mario family characters, after all. Also, had Plusle & Minun and Mewtwo made the cut as originally planned, Brawl would have had eight playable Pokémon.