I recently read this short sci-fi story where this has happened already. The cloned and mix bred neanderthals are superior in many ways. So much so that they become the targets of violent discrimination. Pretty good read.
It was in Gardner Dozois' 2th volume of the years best science fiction. Ted Kosmatka’s “N-Words”
“It was in Gardner Dozois’ 2th volume of the years best science fiction”
That was supposed to be “the 26th volume”