Even though, these alterations would have huge immediate benefits they do have the potential to destroy the human condition and the essence of our identity. So even though the Federation COULD do this, it CHOSES not to. Because the consequences could be far reaching, uncontrollable and destructive.
Except whenever such issues like "uncontrollable and destructive" consequences are brought up, no one brings up any examples. Outside of what humans have done to other humans on Earth, where exactly is there a case of the Prime Directive being ignored and suddenly coming back to bite us in the rear?