As someone said, it's for balance. Not the kind that tries to balance for the sake of metagame, but for mewtwo itself (and many other mega pokemon who got boosts on unnecessary stats)
They can't just make the powercreep worse with extreme tailoring. Flavour wise, these pokemon grow stronger "in every aspect" too, just more focused on certain stuff, instead of being obvious killing machine. Also, LO mewtwo outdoes mmy in damage. MMY has the unnecessary speed, special bulk and durability (and freedom to change attacks)
Not saying it's more viable, I was just listing its actual improvements if u will
Balance is a great theory, but as already stated, MMY is hardly any better than Regular Mewtwo with any sort of decent item. I don't want him to be so insanely OP that he beats any uber ever, but I would like him to be actually better than regular Mewtwo. Isn't that the point of Mega evolutions?
And again, look at him? How the heck does he GAIN 40 attack points? Even with Mega Gardevior, I understand the reasoning of raising the attack. It looks bulkier. MMY just looks frail.
There's nothing that sucks worse that that moment in an argument when you realize that you are wrong.