I now put it at about 5% flawed, but that has undergone an evolution. It started out for me at about 15% flawed. But as I studied the film more, the things that I was impressed with steadily grew in proportion to the things that I wish were done better.
For me what the film lacks, and that is done so brilliantly by the MCU in particular, is truly warm and relatable characters--at least as compared with films like
Captain America: The First Avenger
The Avengers
Iron Man
Guardians of the Galaxy
Star Trek
Star Trek: Into Darkness
X-Men: First Class
Hellboy
Star Wars: The Force Awakens
and I could probably go on and on, but you get the point. (Those are particularly shining examples to me in the character warmth and relatability aspect.)
Again, for me in MoS this is the main missing ingredient: warm and relatable characters. It is not to say that that there is no warmth or relatability to them. But in comparison with the other highly entertaining films listed above as examples, it is lacking.
As for all of the good things that I like about MoS: I love that it is a ballsy reinvention of the Superman myth that brings Superman into the real world--with all the ramifications that that entails. I love that it has some impressive mythic themes deliberately woven into it symbolically. I love the Kryptonian backstory (and its allegory) and worldbuilding. I love the pacing of the story and even its tense and somber mood that ends in a climatic final battle that really does justice to the powers that Superman and Zod have. I love that dramatic moral dilemma that Zod has to be killed as choice of lesser evil--and what that signifies for a character like Superman in the real world. I love the ways that all the characters are developed. I love the acting from everyone in the film. I find the story to be very tightly crafted and internally consistent.
So all of these things I think are masterful, actually and for me they far, far outweigh that one element that I wish the film had: more human warmth that powerfully connects me to the characters directly at the heart level.