I can see Lex being the Loki of the new DCU, he'll appear and cause trouble in various movies but outside the first one i don't see him being the main threat
Brainiac, I think the second movie is to early for him, there wouldn't be enough build up and the first big screen brainiac should come with a bang
Zod- meh he's a boring villain in most media, except young just he was dope in that
Darkseid- I always thought of him as a justice league villain rather than a superman villain
I think the best villain for superman to fight right now would be Amazo
When done right he's powerful enough to push superman to his absolute limits but he's also just a machine meaning he'd be taking orders from someone else which would be a great way to introduce Star labs