He’s one of Superman’s most legendary foes in DC Comics and DC films; given that Supergirl is about Kara rather than Clark, it would make sense that he’d show up to menace National City rather than Metropolis.
By this point, I’d say that plenty of us were expecting Zod to emerge as Kara’s new nemesis for Season 3, and he would make sense.
Now, it sounds like the baddie will be someone we didn’t see coming.
Andrew Kreisberg’s comments give the impression that the big bad for Season 3 will turn up briefly in the finale, and he or she will be somebody we hadn’t seen before and we won’t expect.