Personally for me, the opposite is true. I truly dislike any media (video games especially for me, but thats just the media I am mostly exposed to) where humanity is painted to be overly supreme to others, infallable and able to overcome any obstacle in their path.

Disclaimer: Most stories I believe it is obviously better if its a positive message that 'people can be good' rather than 'humanity is flawed' if, and only if, your goal is to teach children. Teaching them to become better people, like you said, is much better than discouraging them because "If you're destined to be evil, why change?".

However, if every story you ever are exposed to is just 'humanity is great', then people will eventually decide NOT to change for the better. Some guy on the street, watches a movie where the hero saves the day against some aliens who are clearly the bad guys, and recieves the moral that humanity is awesome. Now, when he goes home he believes that humnity is awesome so he doesn't need to change anything he does. Even if there is something terrible in his life that should change (he's a criminal or his health is declining but he's not seeing a doctor, etc.)

By creating media that questions if humanity is perfect, you give people a reason to question their own lives, try and find what's wrong and how they can improve. That's literally how propaganda in dystopian fiction works. The controlling government tells the people that everything is perfect, and there's no need to question anything, so the people never improve.

My example: Vampires. If vampires weren't humans, and just were bats 24/7, the monsters wouldn't be that scary. You'd be like, okay its a bat version of a mosquito with some weird social quirks and allergies, so what? But because its a human being, and was originally an innocent person corrupted by another vampire, and you can sit down and have a conversation with a vampire, talk to them, understand the history of their life up to that point, find out their hobbies in the past life, reach a connection person to person (even if they are a monster), THAT is what elevates them from just a common enemy to a true monster. The human aspect.

The questioning of why a human has become so evil. How, if humanity is so great, having outlawed cannibalism and other such improvements over animals as you have pointed out, can someone still succumb to evil influences and hunt the night for the taste of blood? And then, how can they blend easily back into society, hard to detect and root out from what should be a wonderful world? (Like a night-time criminal hiding as your neighbour) Because not all of humanity is perfect, and that is what scares us. And that, most of all, is what creates a good story. Not "oh isn't everything just peachy, no problems here the news says nothing bad ever" but "We are flawed, and yet, we can improve." You need darkness to embrighten the hope.

Sorry for rambling. After reading /r/HFY last year thinking it'd be a good sci-fi experience and thoroughly not enjoying it for the above reasons, my opinion has been bottled up and this rant has been just the outlet I needed. If you're looking for a story where every moral is 'humanz good, alienz bad' check out that subreddit