5 years ago - When Superman is killed by Doomsday, Cadmus labs accelerates it's attempts to clone him, secretly using Lex Luthor's cloning technology. The Clone reacts to it's rapid growth & learning programs and escapes their custody, severing his ability to ever age. He takes the name Superman for himself, although everyone calls him Superboy. After Superman returns, He relocates to Hawaii.
4 years ago - Superboy joins Young Justice, where he meets Cassie Sandsmark. He begins to develop a relationship with Clark Kent.
3 years ago - Connor has a crush on Traci Thirteen after she helps him in Hawaii. After the battle that killed Donna Troy, Cyborg builds a new Teen Titans which Superboy joins. When Superman opens up to him about his identity, Superboy takes the name Connor Kent, and moves to Smallville to stay with Ma and Pa Kent, where he meets Kara Zor-El. Superman introduces him to 10-year-old Krypto, who comes to stay with him in Smallville.
1 year ago - Connor Kent joins all the surviving Titans on the homeworld of the Titans of Myth to save Donna Troy. He and Cassie Sandsmark begin their relationship.
now - Connor Kent is killed by Hank Henshaw. His remains are sealed in a tomb on mars. He later returns, having been rejuvenated in the future and sent back by Brainiac 5, now able to age. He recovers his own body and entombs it within the Phantom Zone.
2995 - Connor Kent's body is recovered from the Phantom Zone by Querl Dox. He is revived, and re-engineered to allow him to age. After some time with the Legion of Super-Heroes, Querl manages to align his temporal technology to send him back.
While the pre-crisis Superboy has his charm, it's ultimately unsustainable to have Clark have all those adventures as a teenager. It removes the narrative weight of his arrival in Metropolis if he's already been active as a superhero for the better part of a decade. The invention of the post-Byrne Superboy during the Reign of the Supermen was by turns clever and ridiculous for a long time before Geoff Johns crafted him into the character we now recognize in the pages of the Teen Titans, and then from the Young Justice animated series.
I do like the idea that Connor has Lex's DNA, because it becomes part of a larger story about Lex trying to clone Superman, which we all know is happening because Bizarro is a thing.
(Apparently, Johns pitched the idea that Superboy's human parent was Lex Luthor back when he was Richard Donner's assistant and was laughed down... which is funny because he went on to have so much editorial power in DC he could make Lex Luthor EVERYONE'S father and no one can stop him.)
Also, while I've tried to avoid the cliche of characters constantly dying and coming back, in this case I actually like the idea, for several reasons. One, there's absolutely no avoiding the story of the Death of Superman, so it's already canonized that Kryptonians can enter a 'healing coma', so it's not out of the question that Connor might undergo one as well. Two, having Connor gone for a while served a a major character moment for Cassie, and I'd like to retain that. Third, the idea of using his death as a way to have Connor interact with the Legion of Super Heroes fulfills a major gap in THEIR story. It all seems to fit nicely.
I deliberately changed the cause of his death, because I'm trying to avoid any of the Crisis stories, as they invariably break everything. Hank Henshaw is an excellent replacement.