User blog comment:UniverseAwesome777/Ask Universe (for real this time)/@comment-35104290-20190304170108/@comment-26941217-20190306011356

Mewtwo's not just a clone, he's technically a mutant. Dr. Fuji and the rest of the science team fiddled with Mewtwo's genetic coding, which likely changed his appearence drastically.

It's mentioned in the first movie that Giovanni was insisting that the scientists created powerful clones whose powers would surpass that of any other Pokemon, and that "many attempts failed". So through the process of selective breeding and genetic engineering, they were able to create multiple Mew clones before eventually creating the Mewtwo we all know and love.

I'm no Biology teacher though - it's much more in-depth than that.