I don't think this film was as bad as people are making it out to be. It was definitely flawed but not terrible.
For me, the hardest thing to accept was that it didn't FEEL like a superhero movie. It felt like a sci-fi action movie. Thinking back to Batman Begins though, large parts of that didn't really feel like a superhero movie either. It was more about the Man begind the legend of Batman.
So for me, the main flaw is that I don't think this approach necessarily works for Superman. He is supposed to be THE superhero, the quintessential one. I dont want to see a conflicted, tortured loner, at least not to that extent. I want to see someone who rises above it all... I don't think it's the fact that he's an outcast that makes him interesting... I think it's the fact that Supes is an alien, one of the last of his race, who dedicates his WHOLE existence to protecting an entire planet. There is so much potential to explore the psyche of someone doing that, someone who tries to 'save everyone'.
Man of Steel didn't focus on that, in fact it seemed to teach weird morals... That for the greater good, it's okay for people to die if it saves more. The Superman I know wouldn't have let Johnathon Kent die.... He would have IGNORED him and saved him anyway. It would have been a great character moment, to explain to the audience exactly where Supes stands. Superman is the hero who doesn't pick and choose what events are worthy of him, he's the hero who tries to save everyone.