I'm guessing that the A is implying a new legendary or mythical. Or at least hoping!
Besides, I doubt that they'd have four mega evolutions for any one Pokemon. Three, it's believable. Five? Sure. But four? It's just a weird number to have in terms of more powerful variants. If there is to be a Mega Mewtwo A, there's also a *very slim* chance of a Mega Mewtwo W, which would likely bring a legendary or mythical "W" Pokemon. Although, I will admit, it does also sound cool to have something like a Mega Mewtwo V too.
I suppose that the A could also mean the armored Mewtwo from the GO raids awhile back, which I'll admit, I've always wanted in the other games. If Mega Mewtwo Z will exist, it feels as if it makes more sense to have three megas and a special variant instead of four.