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Mega Mewtwo Y's stats: http://i.imgur.com/93sChyp.jpg
Looking at this images, his base Sp. Attk stat is right around 200, maybe a little lower. You may be better off reserving a Mega Stone for another Pokemon.
A Base Stat of 200 will get a Timid Mega Mewtwo Y 499 Sp. Attk. Regular Mewtwo with a Life Orb and Timid nature gets a Sp. Attk stat of 529.
Mega Mewtwo Y is definitely faster though, so how about running him with a Modest nature? Well, judging by this image and as others have pointed out, his Base Speed is right around 140. With a Modest Nature, his max Speed would be about 379, considerably lower than a regular Timid Mewtwo's 394. 1 point in speed is all it takes to lose a match, so this is a pretty sizable difference.
Also, Mega Mewtwo Y's Sp. Attk would be 548, which is not much higher than a Life Orb regular Timid Mewtwo's 529, and certainly not high enough to justify the lost speed. Mega Mewtwo Y will need a Base Speed stat of 148 in order to run a Modest nature with the regular Timid Mewtwo's speed.
So, to summarize, Mega Mewtwo Y with a Speed boosting nature will hit faster but not as hard as regular Mewtwo with a Speed boosting nature and Life Orb. If you run a Sp. Attk boosting nature on Mega Mewtwo Y, he will slightly harder than regular Timid Mewtwo with Life Orb, but won't be as fast.
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The major thing is though unlike LO Megaevo form will not costs health every turn on recoil. Has better SPDF to set up on Calm Mind, but on the other hand takes physical blows in a terrible fashion compared to Normal. (Then again Dat Health isn't bad.)
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