well in the anime mewtwo was created by team rocket as an artificial pokemon. genesect was created by team plasma by reviving an ancient pokemon and upgrading it with cybernetic armor and rocketlaunchers and stuff.
now i havent kept up with the b/w anime but i remember there being a big underground war between rocket and plasma and so it would fit thematically and they could explain how giovanni knows about mewtwo again by having the guy from mastermind of mirage pokemon returning his memories.