Just looking back at Bendis' Man of Steel because I find that book continues to prove that it acts as a forecast to what Bendis is currently doing. There's fairly obvious stuff like Jon's growth spurt and comment about the "Legion of kids that can take care of themselves" foreshadowing the age up, him having to go it alone and take care of himself on Earth-3, and the reintroduction of the Legion.
But if my theory on Zaar being a half kyrtonian comes to pass then Man of Steel seems to have pointed to it pretty hard. Like, now I'm just now realizing that Rogol Zaar and Jon Kent operate on a sort of parallel structure throughout most of the story, and at the end their inter-cutting stories make up all of issue issue 6, and Superman perfectly in the middle of it all. Zaar is what happens when a scared and confused half kryptonian (or any child really) isn't raised with love and understanding. I think that may be partly why Bendis has been so upfront about Jon not coming back bad. It's because the cracked mirror version of him is his uncle.
I noticed that both Jon and Zaar make propositions to their "guardians" (Lois and Clark for Jon, and The Circle for Zaar) and both have ulterior motives when they make there requests. Jon says he wants to leave for space because the Titans didn't accept him and he's scared there may be something wrong with him, but in reality his fear goes far deeper in regrades to his place in the universe, and he's worried about the legacy he'll have to take on. Zaar says that Krypton will wreck the galaxy as it seeks more power, but in reality it's far more personal and (likely) about being abandoned as an El. Even the wording that the "guardians" of both use is mirrored. They talked about how they want to know Zaar was "heard" and how he's not being "ignored." Lois makes sure Jon should never feel bad about expressing himself. And funny enough, both sets of guardians acknowledge (for wildly different reasons obviously) that they wouldn't be able to stop their kids from doing the thing they want to do. Later on in Superman Jon even parallels Zaar preferring to live in solitude in a harsh environment.
I also found it very telling that even though Zaar used Zor-El's device, she'll be the one that sends him to the Zone, and ultimately it's Kara's story to find out about him and the ax, Zaar is written to literally bat Kara way as an annoyance that he'd deal with later almost as a formality, but Clark has his undivided attention and hate. And Zaar specifically says "your bloodline must end once and for all. Just like I once promised Jor-El" Then later he asks if Clark has father and children with anyone on Earth. Half kryptonian children as described by Jor-El are all but impossible.
Clark dealing with the sins of his father, ultimately being his brother's keeper, and trying to make sure the mistakes of the past are not repeated with his son. If this is the case, the this makes Jon critical to the plot down to a conceptual level, but it keeps Clark as clearly our main protagonist who has to right the wrongs.
This would also "half kryptonian" scar on Jon's face is in fact there to mirror his uncle Zaar.