
^ Reminds me of Sephiroth during the famous Nibelheim scene so yeah.

Modest
36/0/0/220/252/0
Ice Beam
Thunderbolt/Thunder
Protect
Psychic
Okay, this motherfucker is no joke. The 220 speed EVs lets him outspeed both Timid Latis and speed+ Gengar and makes a great opener with Rayquaza. Ice Beam puts the fucking hurt on Rayquaza/Latis/Groudon/Exeggutor/Shiftry, Thunderbolt/Thunder 2HKOs Kyogre, especially the latter if you're not using Rayquaza, but then the Swimmers own Mewtwo in that case. Protect is an obvious choice as this is 2vs2.

Modest
36/0/0/220/252/0
Flamethrower/Fire Blast
Ice Beam
Psychic
Thunderbolt/Solarbeam
Sun Mewtwo. Use this on your Groudon teams and believe me there will be pain involved. A 447 SA Fire Blast in the sun is nothing to laugh at, just ask Metagross.

Modest
36/0/0/220/252/0
Thunder
Ice Beam
Protect/Psychic/Recover
Protect/Psychic/Recover
Okay, how I overlooked Rain Mewtwo is beyond me.

Modest
36/0/0/220/252/0
Reflect/Lightscreen
Psychic
Ice Beam/Thunderbolt/Thunder/Protect/Recover
Ice Beam/Thunderbolt/Thunder/Protect/Recover
A slightly more defensive Mewtwo if you really need it. The screens do help a bit.
Other Options:
Calm Mind works, but isnt recommended in the fast paced 2vs2 environment. Mewtwo gets Skill Swap, which can be devastating with all those Swift Swimmers and Chlorophyllists running around, but this is assuming Mewtwo survives. Shadow Ball/HP Dark if you're worried about other Mewtwos.
Allies:
Rayquaza is a godsend imo. Without it, weather teams would just walk right over mewtwo. Of course you can use the Sun set if you plan on using Groudon but be sure to have someone abuse Chlorophyll.
Counters:
Lugia & Ho-oh can wall it somewhat, but they dont really like SE Thunderbolts or your ally's physical moves, if any. Deoxys-F can own you if you're not playing JAA. Blissey and Regice can absorb some hits, but they wont be able to last long, especially Regice if Mewtwo packs Fire Blast. Latis with Soul Dew counter Mewtwo somewhat, otherwise Mewtwo goes Rambo on them. Another Mewtwo can pretty much narrow you down, especially if yours is slower.