Part of it was that they killed off New 52 Superman, and one of the first things they had Post-Crisis Superman doing now that he was crossing over was… being the government’s messenger boy and getting his ass kicked to make other heroes look good . Definitely was a “return to tradition” moment in all the worst ways.
Upside is that means PKJ gets a relatively free hand with Arthur and Atlantis when he does want to cross over, since they’re no other book he will have to coordinate with. Downside is it might be Arthur’s turn to get whacked with the antagonist stick, since there’s no way PKJ will have Clark be the one in the wrong if it comes to blows.
Otherwise the nature of Genesis is one of those simmering background plots. It’s probably connected to Aethyr, the god of the Phantom Zone, but how and to what end is unknown. It’s never been completely forgotten, Genesis keeps being important: it reempowered Superman on Warworld, Conduit went mad from touching it in the backups, and just recently Superman channeling its energy allowed him to manifest new powers against Metallo. It keeps being important even though it hasn’t been the focus.