No offense, but I think that is dramatic overthinking of what's happening. Despite what Geoff done with Rebirth, it's not like we know what the endgame is and what is or isn't being restored. Not to mention while a lot of Post Crisis and Pre-Flashpoints elements were added in, it's not like New 52 continutity was shuffled to the side. For all intents and purposes it is the post-New 52 universe just with more Pre-Flashpoint elements being integrated in. Bendis seems interested in Jon and the relationship, so it's not like he is removing them, just focusing on a different chapter of them. New 52 Superman as a whole wasn't a bad concept, but it just needed to be intergrated in the Reborn stories better.