Based on what we know, Shadow Ball and Hyper Beam are no longer charged moves for Mewtwo, and it is likely that one or two new charged moves will be added.
Ttar is a good counter unless Mewtwo is packing Focus Blast, in which case you're one shotted before getting off three Crunches.
Gengar is a solid counter unless Mewtwo is packing a Psychic move, which will one-shot Gengar, and additionally, Confusion will do a heck of a lot of damage as a fast move.
The final top shelf counter is Mewtwo itself, with Shadow Ball. There's nothing Mewtwo really fears that's left on the list. Focus Blast is resisted, Psychic is resisted (heck, those are the ONLY two types Mewtwo resists), and if Mewtwo gets another, better Psychic move (Future Sight, Psystrike, Psyblast), that will also be resisted.
From experience, it seems likely that they would equip Mewtwo with a good counter move to make it tough on attacking Mewtwos. Shadow Ball was that move in the past, but that's out. So here's my list of possible other good counter moves to Mewtwo.
Bug: Any of the bug quick attacks would be effective, but Bug Buzz has the best DPS*DPE, and as a two bar 90 power move (albeit kind of slow), it would be very painful for Mewtwo. Megahorn, Silver Wind, X-Scizzor, or even Signal Beam could also work. No idea if these moves are in the other games for Mewtwo, but they would be an effective counter.
Dark: Foul Play, Crunch, Dark Pulse would all be strong (in about that order), followed by the anemic Night Slash. Same as above, don't know if Mewtwo can get any of these.
Ghost: Shadow Ball totally dominates this category in DPS*DPE. All the rest are a pale shadow ball of it (pun intended). As such, I expect they won't go this route.
So, given that, I think there's a reasonable chance that Mewtwo will come packing either Bug Buzz or Foul Play. Neither move would overpower the Mewtwo one can capture afterwards, and they would make life difficult for someone who goes in with a squad of 6 SB Mewtwos.
Bug Buzz Mewtwo would be fun because we don't have many good Bug attackers (Pinsir, Scyther and Scizor are strictly third rate, Heracross is way better as a fighting attacker, etc.) For a long time I had a middling IV Scyther with Bug Buzz that I did a lot of damage to Exeggutors with, was a lot of fun to fight with.
Dark Pulse would just add another Dark attacker to the list. Ttar would probably still be tops, but Dark Pulse Mewtwo would have a niche as a generalist, and to go against Dark-weak stuff that has fighting moves.
Like all of us, I'm hoping for Future Sight, Psystrike, Psyblast, or something else to make Mewtwo an even better top Psychic pokemon. (I'm relying on catching some to replace all the ones I TM'd to Shadow Ball. There's still about a half hour to do that if you haven't already). But I strongly suspect that there will be two new moves, and one of them will be a different Mewtwo countermove.
Any thoughts? We'll know in about 45 minutes what the new moves are. Until then, speculate away.
