Why do the stronger enemies in anime/manga tend to look more human?
I am pretty sure this is something that originates from the intention of the medium (film, novel, game) to tell a story.
Weak enemies that are quickly dealt with don't need a fleshed out personality. But strong enemies are often your main antagonists and therefore need a personality, motivations and so on. 
In order for us to understand these motivations the antagonists thought pattern needs to be somewhat human. The more human the physique of a character is the more intuitive it is for that character to also have human thought patterns. This results in the general trend of fictional characters to be more human/anthropomorphised the more important to the story they are.

You might also want to consider that weaker enemies often come in bulk and that killing something is less morally taxing if it dosen't look human.

other observations to back this up:


Cartoons for kids often feature anthropomorphised animals instead of normal animals even if the story doesn't involve combat
Video games with less focus on story and more focus on gamplay don't follow this "trope"