He's book smart due to Jor-El's teachings when he was journeying to Earth.
That doesn't make any sense. If he could remember what he was listening to in there, he could remember his parents. I have major doubts about this conclusion. In any case, we see in MoS that young Clark not only participated in Science Fairs, but he also reads giant books about Plato as a teenager.
He gets picked on his classmates and wishes to use his powers to show them up, but through the teaching of/respect for his father he is convinced that can be of far greater use than petty revenge.
In MoS, we also see that Clark is picked on by his classmates. We see it multiple scenes. First, he overhears kids talking about how he's a freak in elementary school while locked in a closet. Second, Pete Ross bullies him in the school bus before it crashes. Third, he is ambushed by Whitney Fordman and his gang outside of a mechanic's. After each of these incidents, we have additional scenes that develop Clark's character, his motivations, and moral reasoning. In elementary school, his mother teaches him that when he is in distress, to focus on something positive and that gives him comfort. While not teaching him to do good or save people, Martha's patience and love for a child who is strange, which constrasts to how the other people were treating him, instills in him both a way of focusing on the positive and a sense of gratitude or appreciation for compassion. On the bus years later, Lana Lang defends Clark to Pete Ross, the bully. Her pity and compassion is something Clark then rewards by saving her and then replicates by saving Pete Ross. After that incident, Jonathan teaches Clark that his gifts were given to him for a reason, and one day they will be a blessing he can share proudly with the human race. Finally, during Whitney's attack, we see Clark resist using his powers for petty revenge, and we also see Jonathan reinforcing his son's actions immediately afterward as indicitive of good character, which is something Jonathan tells Clark he will have to have if he wants to change the world for the better when he grows up.
He has fun using his powers, as seen in the train scene. He derives enjoyment out of them.
I'm not sure how this is relevant, but in MoS we see Clark enjoy being able to use his powers to teach sexual harrasser, Ludlow, a lesson, and he enjoys the experience of flying. Similar to Superman: The Animated Series, we see Clark mostly anxious about his powers and his Kryptonian heritage until his first flight.
He wants to be able to tell other people about his powers, but admits he shouldn't.
In MoS, Clark is so inclined to use his powers to help people that Jonathan opens his heart to heart with Clark following the bus incident by noting how many times he has had to remind Clark to be cautious. It's a hard lesson for Clark to learn, because as a child it's difficult to think macrocomically rather than the microcosm of your own world, especially when you don't know how truly radical a being you are. That's why Jonathan decides that this is the moment he will finally reveal Clark's alien origins to him which, again, is exactly what happens in S: TAS. Many years later, Lois Lane is able to trace so many good deeds of Clark's that she concludes that he finds it impossible to not use his powers to help people.
It deeply hurts him that despite all of his powers that he is unable to save everyone, specifically his father.
Clark is unable to save his father in MoS as well but to different effect. He learns from that incident that as a hero of his caliber, he isn't as free to make selfish choices as others might be; his choices have worldwide consequences. While this lesson is one Clark remains mindful of in MoS, the lesson of Jonathan's death in Superman I is completely forgotten by the end of the movie when Superman uses his powers to save Lois after he previously failed to do so.
He is searching for his purpose and answers about who he is and where he came from and why.
Obviously, Clark in MoS does this too. It's something he begins to think about as early as 14, but something Jonathan encourages him to do and we see him do for at least a decade. The film even frames the discovery of these answers as the final piece of the puzzle that will help Clark see how he can use his gifts in a public way.
He reluctantly leaves his mother in order to journey to find those answers, but takes his time to make sure she's taken care of before he goes.
Although we don't see Clark make preparations to leave, we do see him discuss his readiness to learn and do more in his argument with Jonathan before the tornado. We also get to see him care enough to reunite with his mother and share things with her once he has found what he was looking for. In that conversation, we see his joy at finding out about his people and the encouragement Martha provides when she says, "The truth about you is beautiful" and the "whole world would see that" someday.
He's dedicated and willing to train for 12 years with Jor-El in order to master his powers and gain the knowledge to become what he was meant to be.
Instead of training we never get to see and which is akin to learning how to be a doctor without actually doing any fieldwork as an intern, Clark in MoS's training is something he acquires from exploring Earth, learning about people, and testing his limits as a hero. He also learns about his Kryptonian heritage and the dreams his biological parents had for him to protect and inspire the people of Earth as a bridge or as the best of both his worlds: Earth and Krypton.
All before he emerges from the Fortress as Superman. This is a big part of the reason why that version was so much more successful than Cavill's. I think a good way of putting it is that Reeve is more human than alien and Cavill is more alien than human.
All of things I've noted about Clark's journey in MoS also occurred before he became Superman. Since MoS did all of the same things, and even more in some respects, than I don't think these points are why Cavill's was less successful or indicative of Cavill's characters being more alien than human. For him, his Clark persona isn't as much of a disguise, and for him, a lot of the lessons he learned were from human peers and from the humans he met along the way. He also sought out the advice of humans like Lois and Father Leone when making big decisions and forms more intimate relationships, like his with Lois. This is a character who embraces and lives authentically as both an alien and a human. In short, I think you're wrong.