When was the last time we even saw Zod? Last *I* saw him was the Super-Bat arc with Ra's, where Zod takes half of Kandor back to New Krypton. I dropped Legion pretty quickly but I wanna say New Krypton was still around and part of the United Planets in the future right? But I don't recall any specifics.
And I agree that Zod works really well as a political frenemy of Clark's. It's a perfect role for Zod, and is a fitting evolution for the character that overlaps nicely with Clark's changes and evolution. Zod involved in United Planets politics is a great place for him to be, and I don't think this has dulled his edge at all. No, if anything, he's more dangerous now. He's still a cold blooded killer, still willing to justify anything if it gets him closer to his goals, but now he's got political clout to back him up; he's not a rogue factor anymore, he has a seat at the UP table, and can convince/intimidate other UP members into doing what he wants, which might not be good news for Clark.
Zod has become for the cosmic side of the Super-verse what President Lex was for the earth side of the Super-verse. And if someone doesn't think that's scary as hell then they need to pay more attention to real world politicians.
I do hope to see House Zod show up under PKJ. The Phaelosians seem like the perfect group for Zod to try and bring back to New Krypton; they've lost their own culture (so Zod can introduce his own brand of Kryptonian culture to them easily) but are ethnically Kryptonian, life on the Warworld has prepared them to embrace Zod's brand of rule, and compared to Mongul, Zod will seem like a worthy, caring leader. Zod could very easily and very quickly end up with an entire population of zealot warriors, tempered in the fires of Warworld and possessing full Kryptonian powers.
As an aside, I've been thinking lately about Kara. I don't think she belongs on earth. Her most interesting stories tend to have her in space or in the future IMO. And I wonder, would it really be so bad if she did leave earth for New Krypton? She could be a mitigating voice there, trying to ensure the entire population doesn't just accept Zod's particular ethos and philosophies. It'd give her a status quo and a mission that defines her, separate from Clark and his world. And I can't imagine why Kara would want to stay on earth when she has a chance to rebuild her people. Sure, Houses El and Zod ended up at odds towards the end of Krypton, but they were allies for many, many years before that.