Juno got it. :k
I am the destroyer,
The unstoppable force. - Mega Man proved unstoppable for Dr. Wily; none of his combat creations proved able to stop him.
My power subverts - He can take the enemy's weapon systems and use it against them.
and has slain thousands. - Just how many enemies, both mooks and Masters, has he destroyed over the course of the games?
My name haunts across centuries,
Ascending into a frightening legend. - The name "Mega Man" is used throughout the franchise, starting with him, where it was a simple name. By the ZX franchise, it had become something more, a title, an idea.
The problem with making a riddle about Mega Man is that he's too obvious. So I figured I might as well view Mega Man in the eyes of the enemies doomed to face him.
It's all yours, Juno.