The decision made in Dear Doctor was morally repulsive, they condemned millions of innocent people to die based on their butterfly effect anxiety.
They also turned the prime directive from a political non-interference principle that it was in every episode except Pen Pals and Homeward to a smug 'Callous bastard' rule.
They made the prime directive into the one part of it that isn't a good idea.
As for humanoid aliens. A) The Chase explains that. B) How do we know we didn't evolve the human from just because it happens to be the most efficient form for an intelligent being on an Earthlike planet? For all we know the humanoid form is a genetic imperative. Now, sexually compatible, yeah that's stupid.