And while I did say that I didn't really care how Superman would be interpreted, I would like to make a comparison point which I thought the original Donner film did brilliantly that this film just squanders. Jonathan Kent's death. In the original, he unexpectedly died of a heart attack that left Clark with a revelation that really fits what I can perceive to be his most generalized super hero characteristic. Even with all his powers he had, he couldn't use them to save his father's life. This shows Clark that life, despite being very precious, is also very fragile to the point where it can all be taken away, even when it didn't have to. So when I see Superman doing his heroics, I see it as someone who really does see not only how precious life is, but also how easy that life is to lose.
I always thought what was relevant about Jonathon's death in STM was that it put one barrier in front of Clark "All my powers, all the things I can do, but I couldn't save him." The death of those he loves is the one thing he can't stop - until of course he turns back time to stop Lois' death. The film uses those two plot points to great effect and makes Jonathon's death part of Clark's character arc.
Unfortunately, upon even minor analysis that character arc doesn't accomplish much - Clark doesn't exactly grow. Basically he cheats his way out of the Kobayashi Maru and never learns to deal with death. Not to mention the logic issues his turning back time creates for the movie in general. But, in the moment, it generally works.
I think most of the problems involved in MoS's scene of Jonathon's death is that like most of the emotional beats in the movie, it's rushed. But it does try to connect back to when Jonathon tells Clark that maybe he'll sometimes have to let people die in order to protect his secret. Interestingly, despite Mark Waid's overall negative (and somewhat self-serving) review of MoS
, he said he really liked Joanthon's death because of the fight Clark and Jonathon have right before it. Basically the last real thing Clark says to Jonathon is "You're not my father!", so he follows Jonathon's order not to save him in order to prove to Jonathon that he is his father, that he has absorbed his lessons and will try to honor them to the best of his ability. That's not a bad moment of emotional growth. And, unlike the Donner films, Clark does have a character arc in MoS - he emerges from the events of the movie with a plan and a direction when he began in a state of confusion and wandering.