I'm pretty sure that Mewtwo's Final Smash will be one of the Mega Mewtwos, which would balance out the super-attack/transformation numbers in the Final Smashes of the Pokemon characters (Pikachu, Jigglypuff and Greninja have super-attacks while Charizard, Lucario and, probably, Mewtwo have transformations).
It'll probably be Y, since that's the one that's been getting all the representation; as much as people want MMX, it's not as pushed commercially as MMY is.
As for an actual moveset...here's what I came up with;
Idle Animations:
Idle 1: Mewtwo stands in place with his fists at his side.
Idle 2: Mewtwo crosses his arms and glares at his foe.
Idle 3: Mewtwo punches his fists together twice, then points at his foe.
Crouched: Mewtwo crouches to the ground and flicks his tail about.
Normals:
Jab: Mewtwo strikes with his hand.
Dash Attack: Mewtwo tackles with his shoulder.
Tilts:
UTilt: Mewtwo does a soft uppercut.
FTilt: Mewtwo quickly floats and thrusts both legs forwards.
DTilt: Mewtwo sweeps his tail in a circle.
Aerials:
UAir: Mewtwo kicks upwards with both legs.
NAir: Mewtwo generates a short EMP burst, causing stun.
DAir: Mewtwo slams his tail downwards, spiking airborne foes.
SAir: Mewtwo lunges forwards with his arms, pushing him in the direction he is currently facing.
Smash Attacks:
USmash (Stone Edge): Mewtwo thrusts a small pillair of rocks up from the ground in front of him.
SSmash (Iron Tail): Mewtwo swings his tail in a circle.
DSmash (Thunder Wave): Mewtwo fires off a short-ranged (ie: only directly beside him), but strong burst of electicity, which behaves similarly to a more powerful version of Zero Suit Samus' neutral B.
Special Attacks:
NB (Thunder Punch): Mewtwo thrusts his fist forwards with an electric charge, which causes stun on hit.
UB (Aerial Ace): Mewtwo flings himself skywards, trapping foes in his wake.
SB (Giga Impact): Mewtwo uses his strength to fly at his foe, dealing heavy damage and knockback if it connects. Missing it will stun Mewtwo for a few seconds, however.
DB (Disable): Mewtwo uses his telepathic powers to overwhelm his foes, stunning them as if their shield had broken. Breaks shields in one hit, but is tricky to land, as it requires eye contact. Missing leaves him open for counterattack.
FINAL SMASH:
Mega Mewtwo Y
In a burst of energy, Mewtwo uses his Mewtwonite Y to Mega Evolve. Mega Mewtwo Y is faster, floatier and stronger than normal, and all of his attacks are at double power for the duration of the Final Smash. Transformation lasts for about 1 minute before reverting.
Custom Specials:
CNB1 (Fire Punch): Mewtwo produces a burst of blue fire from his palm and strikes with it, causing fire damage. This also causes Mewtwo to move forward a bit and is stronger than Thunder Punch.
CNB2 (Ice Punch): Mewtwo freezes his fist and strikes, potentially freezing them. Slower than the other punches, but is stronger to make up for it.
CNB3 (Poison Jab): Mewtwo swiftly jabs with a poison-coated fist, causing foes to have a similar effect to Lip's Stick without the flower. The weakest of the punches, but it strikes the fastest.
CUB1 (Gravity): Mewtwo launches high into the air, but takes increased knockback.
CUB2 (Recover): Mewtwo has a better horizontal recovery, but at the cost of his vertical recovery becoming worse.
CUB3 (Confusion): Mewtwo teleports high into the sky, and can continue to teleport if needed. Can be directed in all eight directions.
CSB1 (Bulldoze): Mewtwo charges with increased power, but the attack becomes slower as a result. The first few frames of the move have super-armor.
CSB2 (Flame Charge): Mewtwo charges with faster speed, but lower power. The flames also burn anybody who comes into contact with them.
CSB3 (Blizzard): Mewtwo charges with extreme power, but horrendous speed. Contact will freeze opponents.
CDB1 (Flash): Mewtwo produces a flash of bright white light that damages more and stuns foes for a shorter length.
CDB2 (Double Team): Mewtwo makes an illusion of himself and teleports behind his foe, striking them if they attack the illusion.
CDB3 (Facade): Mewtwo glows with energy, and when hit is "stunned". When attacked while in this psuedo-stun state, Mewtwo suddenly strikes with a ferocious punch, dealing a decent amount of damage and high knockback.
Taunts:
Up Taunt: Mewtwo hovers into the air and laughs.
Side Taunt: Mewtwo scoffs and spins in a circle.
Down Taunt: Mewtwo growls as his eyes glow blue.
Victory Poses:
Pose 1: Mewtwo laughs and proclaims his superiority.
Pose 2: Mewtwo makes a snide remark on the inferior skill of his foes.
Pose 3: Mewtwo proclaims himself to be the ultimate fighter.
Pose 4: Mewtwo teleports in and laughs maniacally with glowing eyes.
Victory Theme:
A shortened version of this;
Trophy Descriptions:
Classic Mode:
"The Genetic Pokémon, Mewtwo is the result of cloning experimentation; created after years of research by a lone scientist on Cinnibar Island. Mewtwo is cloned from the DNA of the legendary Mew, and as a result is incredibly powerful. It's telekinetic and psychokinetic power is extraordinary. Mewtwo believes itself superior to all others, human and Pokémon alike."
All-Star Mode:
"Mewtwo has high power and great coverage, making him one of the most powerful fighters in Smash. Thunder Punch has good power and stuns foes, while Aerial Ace allows Mewtwo to recover large vertical distances with ease. Giga Impact is incredibly strong, but a risky move; if missed, he becomes stunned and open for attack. Disable is excellent for beginning a combo, and when used right, can shatter a shield in one hit; but, like Giga Impact, leaves him open when it misses. With customization options like Poison Jab and Confusion, Mewtwo is versatile enough to match most of his encounters with ease. Be careful, though; Mewtwo is strong, but not very heavy."
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