I actually opened this thread Saturday so I could make a post. A truly vicious twist came to mind that fit in with this idea. I have a rough outline. Maybe with WFH I'll be able to get it written soon.
EDIT: I have to do some adulting here. I have too many RL irons in the fire. I love this idea but it might take me to 2030 to write it so I am releasing this plot bunny into the wild. If I write my version someday, fine. If it strikes your fancy now, please do with it what you will.
I'd love the scene where "Clark" woke up one random morning in Luthor's cloning tank with a set of Clark's memories and the full knowledge of who Luthor is. He might be confused as to how he got there, but he'd have to decide whether to smash his way out or to bide his time and gather enough information to totally destroy Luthor. Either way, it would be interesting.
Clark was raised an orphan. Martha and Jonathan are fantastic parents but there is always the wondering what happened and why. When he experiences the globe's messages they ground him and give him an attachment to Jor-El and Lara that he realizes that he has been missing his whole life. He can't get the messages to play either by design or ignorance of the controls but he thinks of his family and their sacrifice often.
"Clark" wakes up in Vatman's tank. Kryptonians are telepathic. Both Clark and Vatman are untrained telepaths and are duplicates of each other which makes communication easier. In this case, a half-awake Clark connects with the clone and experiences Vatman's surroundings, the cocoon and the laboratory in first-person. He realizes part of what is going on but is too shocked by the experience to do anything. Luthor comes in and continues the indoctrination of his clone. Something about the physical situation and the message gives Clark a strange sense of deja vu. While Luthor is speaking Clark gets momentary glimpses of another face. Clark isn't sure whether these are his memories or the clone's.
During his encounters with Baron Sunday later, Clark re-experiences being put into the capsule several times. As in the series, Lois points out that he was saved by this experience and he recovers from Baron Sunday’s terrors. During a replay of the memory he sees damage in the background that he assumes is due to the the planet's impending demise. The scene he sees is very similar to the globe message but slightly different from what he expected. Though it is only visible for a fraction of a second, because of the repeats he finally realizes that the face of the man who put him in the capsule wasn't Jor-el's. With further clarity he realizes that when he was placed into the capsule the man was expressing sentiments very close to Luthor’s lessons for Vatman.
When the New Kryptonians arrive one of their leaders shares that same face--Lord Nor. He also realizes that what he assumed was earthquake damage in the laboratory was probably closer to battlefield damage. He is forced to the conclusion that in the last days of Krypton, Lord Nor overpowered Jor-EL and placed his own son into Jor-El's capsule to save him.
Clark's whole world is shaken. Jonathan and Martha raised him to be honorable but survivor's guilt is mixed with shame at taking the place of Kal-El. Is he worthy of being Superman? How can Superman stand for truth and justice when his very existence is due to a despicable act of an evil man? Who can he even tell? In light of what he knows, what should he do about the New Kryptonians?