Depends on the form. But anyway:
Deoxys (R/S): Tie. Deoxys has high Spd and both great offensive stats, but low defensive stats for Mewtwo to get it with a good attack.
Deoxys (FR): Tie, probably, but more towards Deoxys. High Spd, and god awesome offensive stats. Mewtwo could lose, but it might win with Deoxys' crippled defense.
Deoxys (LG): Deoxys. Can take Mewtwo's attacks and either stall it or use a thunder wave and hope for a victory with switching into a sweeper, regardless of it's speed.
Deoxys (E): Dunno. Tie, maybe? It's offense and defense is average, yet it's Spd is really high, so it's kinda hard to tell.