Really dont get that comment.
As for the rest, I cant agree, the comedy really hurt Iron Man 3 at essential times, like then Tony makes a joke 3 mins after Pepper supposedly dies, the woman who apparently is the most important thing in the world according to him. There were other moments as well and moments that should have been given more importance, like the arc reactor removal and Rhodey's role was one big joke.
MOS had Superman having to accept mankind and earth as his home and his people ahead of the race that gave birth to him. A few times he has to choose between remnants of his home world and his adopted one and he has to think about it every time. He earns the trust and faith of a whole planet by fighting for it with all his might.
Then there is the question as a child as to his nature and who he will grow up to be and how the Kents try and steer that in the right direction and then also finding out his parentage and choosing to stand proud in front of the human race despite their initial fear of them.
Making the choice of destroying any chance of Krypton being re-born to save humanity at the is the culmination of all this. MOS has a lot more substance than people give it credit for. It knew the importance of its emotional scenes as well by not throwing in a joke 3 mins after them.
I think the problem most people, including myself, have with Man of Steel is not that they don't understand what it was going for (essentially, what you just described) but rather that it failed to make any of these things work on a dramatic or interesting level.
The problem with trying to hang the story on Clark's choice between Earth and Krypton is that the film does a terrible job of convincing anyone that the choice would be difficult. This is partly because the choice isn't Earth or Krypton, it's genocide or a brand new Krypton alongside eugenics hungry criminals. The film makes the choice asinine by highlighting at every point that Clark always saves lives, even of people he doesn't like (unless they choose otherwise). Always, that's just what he does. Therefore, the critical moment in the film that's supposed to define the character as Superman arrives, and it's not remotely cathartic, exciting or interesting. It's a rote conclusion.
It may have been possible to convince an audience Clark would be into genocide if the film had offered a compelling reason that he feels alienated. All the film can muster though is 'because he has superpowers'. That's about as shallow a conflict as it gets, in this case. The film shows us he has loving relationships with at least his parents so he's clearly capable of finding them. If the film had explored any reasons why Clark couldn't form any worthwhile attachment to Earth, then it might mean something when he chose Earth.
These are pretty crippling flaws on their own, and that's not even getting into the mess that was Kryptonian society, the codex and all that predestination vagueness. People say Man of Steel lacks substance because it fails to make any of the (few) choices Clark make matter.