Disable shouldn't be an issue, should it? Deku Nut is an example of something that can already automatically put a person into their "shield broken" state, and it would work mechanically the same as a modified Sing (although making it have knockback only when the enemy is stunned or in a tumble already as it was in Melee may prove difficult).
I don't want Disable to be changed. It was a neat mindgame move and it can easily be balanced by modifying how safe it is to throw out VS how long the enemy stays stunned. I wouldn't mind switching it to side-B and Confusion to down-B, though, depending on what we replacing Confusion with.
Low-lag non-freefall Teleport sounds awesome and I fully support it.
Giving Mewtwo only a directional airdodge seems like a pretty stupid if not downright impossible concept. He should definitely retain his disappearing animation, though.
Confusion would be confusing to program and a big waste of time to reimplement, and any buffs to it so you could guarantee a hit from it would just make it Disable With a Different Animation (including making the opponent trip). A decent amount of the replacements discussed so far could be good; I favor Recover in particular, especially one of the implementations stingers suggested. And no, direct recovery moves are not broken by default. There's no reason, when properly balanced, that they have to break the game.
Any type of replacement we do decide on for Confusion shouldn't be a projectile, as Mewtwo already has Shadow Ball and shouldn't be a projectile-reliant character. Some type of move that charges itself naturally as the match progresses like Wario's waft would be neat; I'm thinking an implementation of Return in the form of a quick attack that hits in a circular perimeter around Mewtwo, and as the match progresses its range and power get larger. Other neat ideas are Taunt (causes the opponent to lose the ability to use special moves for awhile), Secret Power (randomly causes some type of effect like flowered, buried or frozen), Reflect (obvious), Skill Swap (takes the side/down B of the opponent a la Kirby's swallow), Fling (tosses picked up projectiles with extra force and damage), Amnesia (causes you to take less knockback/damage for a time period), and Sleep Talk (basic physical move that can be used when you're stunned or asleep).
Why should fthrow necessarily be changed? Replacing it with some type of Swift sounds neat, but mechanically we already have a way to spawn projectiles during a throw (Falco's, Fox's), so I don't see why it needs to be replaced. Regardless, it's not exactly his most iconic move, so replacing it wouldn't be a big loss. As far as how the move works, I say it should be Mewtwo's most damaging throw, to offset it from uthrow for killing, dthrow for combos and bthrow for positioning. Homing Swift stars seems like a good way to guarantee that damage as well as make it a unique move and possibly set up for a combo while the opponent is still stunned by the stars.
As far as his Final Smash goes, we don't really know what we'll be able to do with PSA for final smashes yet, so the safer guesses would be the attacks one of the legendary Pokemon from the Pokeballs, like Lugia's or Deoxys'. If we have enough power, any of Mewtwo's big, powerful attacks that can either hit one opponent hard or cause mass destruction across the stage could be used: Thunder, Blizzard, Focus Blast, Hyper Beam, Earthquake, Rock Slide, Fire Blast, Avalanche, just to name a few. It could also be an adaptation of stage or item effects, like slowing down time for all the other players or reversing the other players' controls. If we can get fancy enough, something that literally allows him to control his opponent psychically would be amazing.
I'm not sure if we can keep his quirky double jump mechanics, but that would also be a good feature.
He should definitely be a floaty heavy a la Samus. Being his size AND lightweight is a completely bull**** weakness.