So what--Superman had no real internal struggles from two father-figures? Superman was just mopey because... of angst?
He was mopey because it was hard to grow up so different with so many responsibilities. The choices he makes have bigger consequences. People like his peers and Pete's mom respond to him differently than they would to normal humans. His internal struggle is about identity and trust. He struggles with figuring out who he wants to be and who he is going to trust.
I mean he was on a journey for something. If both fathers complemented each other would he be less confused or unsure. I never got the feeling that Superman was completely supported by anyone. His reluctance to act when necessary felt that it came from Jonathan. After all, it's one of the more memorable scenes when Jonathan said, "Maybe" in regards to letting those children die.
Clark was never reluctant to act. Whenever it was necessary to act, he acted. The only time he held back was to let his father sacrifice his life for his future. Superman was completely supported by Martha, Jonathan, Jor-El, Lois, and Father Leone. Clark was confused and unsure because he was a young person trying to figure out how to share his blessings with the world and when it would be the best time to become a public superhero. Those pressures were pressures placed on Clark from the nature of life itself. These are the same pressures we all struggle with in our lives but on a much larger scale.
Jonathan's "Maybe" was a not a "No." He did not teach his son not to help people or save kids on flooding buses. Jonathan taught his son to think about a crisis and think about the consequences of the choices he makes. He wanted him to know that sometimes you think you are doing the right thing when, for example, you dam up a river to save your farm, but there could be unforeseen consequences like flooding the Lang farm, or as it was with saving the kids on the bus, religious fanaticism from Mrs. Ross. Jonathan followed up his "Maybe" with this:
There's more at stake here than just our lives, Clark, or the lives of those around us. When the world...When the world finds out what you can do it's going to change everything. Our...Our beliefs, our notions of what it means to be human. Everything. You saw how Pete's mom reacted, right?
Jonathan is teaching his son to think big picture. He's not telling his son he should not help people no matter what the circumstances. He's telling his son that there is no way he can give him all the answers. He reiterates the same idea right before the tornado hits. Jonathan repeatedly tells Clark that he doesn't have the answers. All he knows is that Clark is so different and so special that the choices he makes will change the world, so Clark's tentative approach to life is born out of his need to use his powers humbly, judiciously, and carefully.
I mean, the audience members can't simply shake that scenes or the tornado scene and reach a conclusion similar to yours. Especially if the context is as subtle as you're making it out to be.
I'm not making out anything. These are the facts of the film. This is the verbatim dialogue from the film. I'm not reaching conclusions. I'm citing facts. If audiences see red when the color is blue, I don't know how to help them. Jonathan literally tells Clark the exact same things Jor-El tells him and yet the audience comes to completely different conclusions about each of these men as fathers.
Jonathan Kent: But you're not just anyone, Clark, and I have to believe that you were...That you were sent here for a reason. All these changes that you're going through, one day...One day you're going think of them as a blessing. When that day comes...you have to make a choice. A choice of whether to stand proud in front of the human race or not.
Jor-El: You will give the people of Earth an ideal to strive towards. They'll race behind you. They will stumble. They will fall. But in time, they will join you in the sun, Kal. In time, you will help them accomplish wonders. [...] We wanted you to learn what it meant to be human first, so that one day, when the time was right, you could be the bridge between two peoples.
The tornado scene is a scene about Jonathan wanting his 17 year-old son to have the freedom to choose for himself when it's the right time to debut as Superman. It's about Jonathan admitting he doesn't have all the answers. He's making it up as he goes along. It's about Jonathan recognizing "Maybe our best isn't good enough anymore." This isn't the "context" I am "making out." It
is the context. It's not subtle. Word for word dialogue isn't subtle.
(And look... this is all coming from memory... I'm not reaching for any conclusion through any formal studies of the human psyche with these... because, frankly, these stories are rather 2 dimensional and pretty generic at the time of the films release.)
These aren't conclusions that must be reached through formal studies of the human psyche. It's just the dialogue in the film. It's really simple.