So the set-up for next season could potentially be(all speculation on my part)...
1) Clark taking a leadership role and really becoming a true hero(heard that before).
2) Chloe dying(dunno, could happen).
3) Martha Kent as some sort of super spy/politico "Red Queen"(it would give her more to do than just be Clark's mother figure I guess).
4) Tess, Oliver and Lois all staying more or less as they are currently.
5) Zod, the only real question mark in my mind. I would love to see a bait and switch and Zod become a good guy(or die a noble death against this "new" threat).
6) Which of course leads us to this new threat. If it is Apocolypse as has been hinted at that could be fun.