First let me start by saying that I really liked Man of Steel. It got me into reading Superman comics. I think the bulk of my expectations came from Hans Zimmer's soundtrack more than anything. For me I benefited from not having an exact idea of what "my perfect Superman movie" would be. All I knew is that I wanted it to not be Superman Returns and I wanted it to be a movie that could stand up to Batman.
That is the first problem. Following Batman. Universally loved character. He is like the rebel of Superheroes. I mean, don't get me wrong, I love the Bat, he is my personal favorite, but I am going to be as objective as possible here. The perception with Batman is that people can relate to him, which I find interesting because no one I know had their billionaire parents shot dead and had to overcome that, nor have they devoted their lives to serving justice, but I get it. He isn't an alien, he isn't a mutant, isn't a super soldier, not using a high-tech suit (though he does use high-tech gadgets). So you have basically the polar opposite of all of that in Man of Steel.
I put Superman in the Incredible Hulk class of really hard movies to pull off perfectly. There is still the crowd (Batman is victim to this crowd also) who LOVE the 70's version of Superman and this new, dark, "emo" as they would call it version just isn't what they know and love. Then you throw in the awful generalization that he is invulnerable to anything, overpowered, yadda, yadda, yadda and that is boring, and it would be if that's all we were served. I will even say about Superman Returns that we got more than that. Every character has to have a decent story. I think people don't even try to relate to Superman, but it's amazing there is just as much to relate to. He's an orphan who has to deal with fitting in, parental issues, general being a man issues. Then there's the debate of is the man really Clark Kent and Superman is his alter ego or is the man Superman and Clark Kent is his alter ego and that to me is interesting.
For me, Man of Steel is very similar to Captain America. Everyone I know personally minus my immediate family and best friend just did not care for "First Avenger". They find the character boring, too much of a boy scout especially in comparison to Iron Man (Iron Man/Captain America is Marvels Batman/Superman). In fact I am writing this because I have fought for First Avengers' status in Phase 1 for years and now all of the sudden people LOVE Captain America (convenient). So bottom line, I think that's what it takes. Man of Steel was the trial by fire, so to speak. It wasn't terrible by any means, most of the complaints were due to the destruction, which is bizarre to me but I think given time and the other movies coming out between them, it will give it a chance to breathe. I don't know if Man of Steel will ever truly get it's due, or what I think is it's due, but I definitely think Superman/Batman will be received far greater and when I say that, I want to specify that people will walk away liking Superman much, much better, if not outright loving him. This, of course, depends all in how it's written and it could be written terribly, but if it is an extension of Man of Steel, in the same vein, I think people are going to be warmed up to the character and really appreciate him and once that has happened if they go back and give Man of Steel a shot, they will enjoy it more.