A neat idea, but one wouldn't want t' take away from Snake's unique stage control.
Down-B could be somethin' simple, like a projectile reflector in the form of Magic Coat (which means the loss of Confusion's ability to "reflect" projectiles wouldn't be missed). Or perhaps Recover; Ivysaur has Synthesis, so I don't see why not. Synthesis' biggest draw is it's Solarbeam charging, so givin' Mewtwo a notably quicker healing rate would be neat. Maybe it could be Barrier, which creates a small, immovable, physically-impassable wall which soaks up a specific amount of damage 'til it breaks. It'd be a cool edgeguarding tool. Or maybe he could use Reflect and Light Screen in one move, tap or press of B determining which. Reflect is the one that soaks damage and can't be passed through, 'cept projectiles. Light Screen absorbs projectiles and eventually breaks, but can be walked or physically attacked through. For balancing purposes, I'd imagine only one screen could come out at a time, and both would be easily distinguishable by appearance.
Future Sight could also be an attack that strikes an opponent wherever they are with acceptable tracking after a specific amount of time (probably not flexible t' keep it from bein' broken), unless Mewtwo is damaged before the attack hits. Could make for some crazy combo resets like with Din's Fire. I can imagine comboing someone off-stage into Future Sight -> D-air t' be pretty nasty.
Perhaps rather than a set time of automatic detonation, after a waiting period of usin' the move Mewtwo can cancel on-hit into it for a combo extension/finisher. This would keep the move from bein' spammable like my Future Sight's first concept would be. Along with Shadow Ball, would give opponent more reason to not give Mewtwo any space. Would also give Mewtwo some extra guaranteed damage on projectile characters once he manages t' get in.
... I just realized somethin'. What's Roy's Final Smash gonna be?