Not sure how obvious this is ...But Superboy-Prime (post-Crisis) is This Loser Is You and sort of a Take That! to the prototypical 'comic book nerd' and their opinions on comics.
Should Superboy-Prime return, he will be a meta-fiction wielding Well-Intentioned Extremist.As of Adventure Comics #4 and #5, Superboy Prime has begun to realise how bad he's become, and also gone to hating the writers instead of the characters. Due to the reboot, he'll survive and realise that the writers were once again manipulating him(specifically with Black Lantern Laurie), and begin to empathize with the characters in the New 52 about how they're being "manipulated." He will do this by trying to band together Superboy and his friends, and find a way to ultimately take down the writers, or at the very least make it so that the characters are "free" from us, through whatever means necessary. Due to becoming Genre Savvy, he'll likely disguise himself as another of Cadmus' projects/a second Superboy to hide under the reader's noses. This would have the bonus effect of Superboy-Prime becoming an endearing character while remaining a villian. Not to mention that, given how Superboy has had a history of being manipulated, it'll make Superboy Prime a more effective Evil Counterpart.
The clone thing is just a cover story. Kon-El is actually the result of Superman and Lex Luthor having a secret Dating Catwoman affair years agoSomeone had to say it!