Okay before I start listing the pros and cons for them I have to say thanks to Hoggie3 for giving me this idea go check him out. I'm currently reading his friendzoned story and I already love it.

pros for mewtwo x 

It gains the fighting type 

Its attack defense and special defense get raised

It gets the ability steadfast which makes makes the Pokemons speed go up if it flinches

Loses bug and dark type weakness 

Damaged less by rock attacks

cons

Still part psychic type so the raise in attack won"t help because most psychic type moves are special 

Isn't the form mewtwo uses for his final smash in super smash bros for 3ds and wii u

Is now weak to flying and fairy 

Is now damaged more by psychic attacks 

Only physical move it can learn is psycho cut at level 36 

pros of mewtwo y

Raises attack, special attack, special defense, and speed

Is the form mewtwo uses for his final smash in super smash bros for 3ds and wii u

Gets the ability Insomnia which prevents the pokemon from falling asleep

cons 

Lowers defense 

Keeps same weaknesses 

Was the first one that I saw a funny picture where patrick from spongebob had a caption saying we should put mewtwos tail and put it somewhere else 

So which one do I use in battle Mega mewtwo Y 

Now if you have a suggestion for 2 other pokemon to do next comment it they don't have to be mega forms 

And once again thanks to Hoggie3 for suggesting this and go check him out bye