Two Moves, that's impossible because Mewtwo has 3 Weaknesses being Bug, Dark, and Ghost. So you will need 3 moves to cover its 3 weaknesses. 3 moves that benefit from its SP Attack and covers weaknesses are:
1.Flamethrower- it covers its Bug weakness.95 Base Power and 100 accuracy, its a must have on Mewtwo
2.Aura Sphere- it covers its Dark weakness.90 Base Power and it never misses, another must have on it.
3.Shadow Ball- it covers its Ghost weakness.80 Base Power and 100 accuracy, its the best move to cover the Ghost Weakness.
So that is what I recommend.