I'm pretty much on the scope that none of you really get how Pokémon characters are chosen. Especially jarring since Sakurai actually gave us insight on that.
It's not by representing different generations.
It's not by which ones are "important". (Save for one exception)
It's by whichever Pokémon are the "hot ticket". The ones mass marketed, the ones starring in movies, the ones infamous to the world, etc. (Although they also had to be unique as well as a "hot ticket".)
Pokémon Trainer is arguably the only exception to this (outside of Charizard). Trainer was more or less a unique gimmick he wanted to make, and Trainers are rather important to the franchise.
Pikachu is the series mascot, making it the permanent "hot ticket".
Jigglypuff was somewhat a hot ticket back in the day, but really fell hard, which is why it was a low priority in Brawl, and likely to be so again for Smash 4.
Mewtwo was the star of the very first movie and had quite a bit of promotion. However, by Brawl's time, Mewtwo started to fade as other Legendaries took spotlight, explaining why Mewtwo was low priority (and sadly one of the cuts) for Brawl.
Pichu, while added as a late addition joke character clone, was marketed quite a bit in Gen. 2's lifetime. It still was marketed (and still is) alongside its older "cousin" Pikachu since then, but the concept of a joke character clone was arguably a turn-off, and was thus not even considered for Brawl.
Lucario, was the latest movie star by the time Sakurai decided upon Brawl's roster, and was heavily marketed as a mascot for Gen. 4. It still is being marketed to this day, and we're on Gen. 6 now.
There hasn't been a real new "hot ticket" outside of stars of various movies since Lucario. And unlike Lucario, these stars fall as just flavors of the month. Zoroark was the closest one to being a "hot ticket", but Zoroark never really caught on like Lucario did. It makes it even worse when Lucario was brought back into promotion since its successor failed to achieve the same level of fame. Not even Gen. 6 has a "hot ticket" at this point (though that may change in the future after X/Y are released, but it will be too late to influence Smash).
But at the very least, Mewtwo has climbed back up to the top, especially with being the star of the most recent movie (yes, I am aware it's a separate one from the first movie; I'm talking the species in general), showcasing the new Mega Evolutions of Gen. 6 to boot. Hell, it even has TWO Mega Evolutions, something that no other Pokémon has (at this point in time).
So, to give this rant some more meaning, I am now going to express what I feel will be the outcome of Brawl's Pokémon plus Mewtwo.
-Pikachu: Already confirmed, and obviously going nowhere.
-Jigglypuff: Will be low-priority just like in Brawl.
-Mewtwo: Will NOT be low-priority again, and will be higher priority than Lucario for the same reason that Lucario was higher priority than Mewtwo in Brawl. Also likely to have Mega Mewtwo Y somewhere (Mega Mewtwo X is very iffy considering the late reveal).
-Pokémon Trainer: Undeterminable. It really depends on if Sakurai can recreate the 3-in-1 gimmick he had in Brawl or not. Unlikely to be replaced with a new Trainer/Pokémon set if he can, however. Worst case scenario is that Charizard flies solo (no pun intended).
-Lucario: Will be lower priority than Mewtwo, but higher priority than Jigglypuff due to being more marketable.
As for any others, anyone not named "Genesect" is not happening, and Genesect isn't particularly likely at this point either due to the inevitable curse that is "flavor of the month".