At one point I would have thought Pokemon would be the second headache series to tackle, but everyone seems to agree Brawl + Mewtwo now.
That's because a lot has changed in the past few months.
Mewtwo getting a new form and movie made him the heir apparent to the Pokemon "newcomer" slot.
This conflicted with Sakurai's warnings that the roster would not grow by a large amount and that cuts would be made. People projected that either Lucario or Pokemon Trainer would be cut. There was also talk of Jigglypuff being at risk, the reasoning for which being that her protected veteran status had outlived her novelty as a joke character in some people's eyes.
However, Lucario and Pokemon Trainer (specifically Charizard) are some of the the most popular Pokemon characters of all time, easily comparable to Mewtwo, and Jigglypuff has been in Smash Brothers long enough to garner a very committed cult following. Cutting any of them would cause as big a stink as failing to include Mewtwo, meaning there was no right answer. This caused doubt that there would be any Pokemon cuts at all.
Finally, all worries were assuaged after several official Pokemon X/Y reveals gave mega evolutions to Lucario and all the Kanto starters, as well as a new typing for Jigglypuff. With the the lot of veterans remaining both popular and relevant to current Pokemon happenings, it became increasingly hard to imagine SSB4 without Mewtwo and all of Brawl's Pokemon.
Despite all this, Chrono will probably withhold his judgement until after a possible Pokemon reveal this October, in order to avoid the remote chance of analyzing incorrectly and making a fool of himself.
Personally, the only cut I imagine being within the realm of possibility is Squirtle and Ivysaur being ousted in favor of Charizard becoming an independent fighter.