Greymon has his Omnimon form which is easily one of the strongest Digimon in existence while Mewtwo is the strongest Pokemon in existence. (Passing Deoxys thanks to his new Mega form) These two fighters are immensely powerful and it would be a great battle of destructive proportions. That being said, Mewtwo’s speed in his Mega form will be what changes the tides of battle. Omnimon has a lot of attack power and his beams may even be able to overtake Mewtwo’s, but Mewtwo has the decisive edge in speed which will lead to his victory. Mewtwo wins.
Update: May 29th 2014. Omnimon may not be enough, but Greymon does possess Shining Greymon and its Ruin Mode along with the Crimson form. That will be enough to take down Mewtwo in the long run. Greymon wins.
Original image found in the link below. Drawn by Nyiaj