This direct encouraged my support for Mewtwo, and I thought this would be the obvious reaction.
1. He was not included in any Pokeballs in the vast array of legendaries/normal pokemon shown. Mewtwo is one of the most famous legendaries and just outright pokemon to exist, why not include him?
2. Zoroark deconfirmed(arguably the best pkmn rivaling his spot).
3. Brawl had 6 Pokemon characters. That is without question. The only counter-point I see being made is that "three characters were one slot so therefore only 5 pkmn accepted max." That is incredibly faulty and weak to me. Let's examine the Zelda series. Zelda would be considered one character until this direct according to this logic. Now we have gained an "extra Zelda series character" according to this slot-logic, since Sheik has her own slot. It just isn't a good basis, and that shows that Sakurai views multiple-character slots as what they are; individual characters that so happen to be merged in one slot. A multiple-character slot = multiple, individual characters. It just seems obvious. Characters > Slots
However, I will make it harder for Mewtwo by yet and still using the "Mario series slot-logic."
So here's the worst, most-limited-yet-realistic scenario for Mewtwo:
1 - Pikachu - 2 - Lucario - 3 - Charizard - 4 - Greninja - 5 - Jigglypuff(debatable)....So that makes 5 characters, equal to Mario series(as of now)..but we had 6 in Brawl, MORE POKEMON CHARACTERS THAN THE MARO SERIES(or less, if you count DK and the like, which just further illustrates the arbitrarity of aligning Mario's slot # vs Pkmn's slot #) . Who's going to fill the last slot? A lone Squirtle or Ivy? Hell no. Zoroark is out of the question. Bowser Jr is still possible for a 6th Mario rep, so there's that. Sakurai implementing 6 Pokemon characters is not foreign to Smash, he's done it before and can and will do it again. Mario series got a slot boost, Zelda series got a slot "boost"(by Sheik), so Pokemon getting a 6th slot for Smash 4 really isn't reaching in the slightest. Ironically, 6 pkmn characters for Smash 4 is asking less of what the Mario series got, +1. This merely stays at a comfortable and fitting 6 Pokemon, perfect room for Mewtwo.
4. Mewtwo still hasn't been revealed/deconfirmed/hinted in any way yet. Not a ironclad argument, but still supports the notion of a big-deal announcement at E3 for a big-deal character. This is just present-day evidence that really seems to lean towards this notion. Sakurai already confirmed to us he knows there is big desire for Mewtwo, and therefore is aware of his inclusion in Smash 4. It's obvious he's going into the game, it's just a how at this point. He has way too much support to be totally ignored. Similar to, but better than Ridley's current state.
------
Let me address Sakurai's trifecta of Grass, Water, and Fire type Pokemon. This was a very nice way to represent the elements of the Pokemon series in Brawl and Sakurai obviously noticed because he implemented it. We have Fire(Charizard), Water(Greninja), but no Grass. So if Sakurai wants this again, and I assume it's quite an elephant in the pokemon room, adding a new grass type starter isn't far-fetched. So this seems to lean towards the idea of Sakurai being almost obligated to add at least 6 slots to Pokemon, based on a worst case scenario for Mewtwo(Jiggly's return, which may not happen).
So it would then be:
1 - Pikachu - 2 - Charizard - 3 - Greninja - 4 - Jigglypuff - 5 - Lucario - 6 - Grass pkmn (7 - Mewtwo)
This, believe it or not, would still be technically in line with the treatment of the Mario series. And this supports the notion of 6 pkmn slots in Smash 4, more slots than current-Mario. But we had 6 Pokemon characters before, so a +1(like Mario) would equal 7, perfect room for Mewtwo.
Obviously, if I'm wrong and he wants to do away with this trifecta-idea, then Mewtwo's chances are evermore improved because it's one less slot being filled, even though it really doesn't matter. I'm just using that as the strictest measures for Mewtwo. It seems to me, on all fronts, there is ample space and possibility for Mewtwo even with the most unkind scenarios I present.