Eh, I was never a fan of the nigh-invincible aspect of Superman, whether in All-Star or the Golden Age. It's very hard to pull off, and it usually ends with most of his badguys being pushovers in comparison and it then usually embraces the alien-who-is-aloof interpretation, which usually means that while he keeps his dignity and coolness, he kind of lacks some of that down-home humanity that I've grown to love.
But as for Zod, Luthor, Brainiac, and Doomsday. Here's what I'm hoping:
Zod: I kind of like the idea of Zod seeming very sane and honorable in most ways, and maybe just being at odds with Jor-El when they go to war. Picture a Zod who is a fascist, but likes to think of himself as a reluctant one, and who feels his actions will be justified because he thinks that he could have saved his planet and he now needs to preserve "true Kryptonian ideals" on Earth. He doesn't hate humans necessarily; he just feels they should kneel before their superiors. He genuinely can't comprehend why Jor-El and his son would fight to let the weak choose their own destiny, and is at once both saddened and enraged by their continual interference.
Brainiac- Eldritch Abomination who just won't die. In every way that Luthor is the worst known aspects of humanity, Brainiac is everything frighteningly unknown about aliens. It only puts on the fascimile of humanity and humanoid behavior, and it lives as data, which is all but impossible to destroy.
Lex Luthor- Needs to be built up and then shown as a massive threat and the worst of us. Despite his humanity, Lex should be able to hurt Superman in so many ways that are beyond, but not excluding, physical pain. If they could include something like him trying to corrupt Supergirl or sending Superboy as a Manchurian agent who he can then flip into killer mode, that would be a good way to show just how bitter and powerful he can be. Even if he is taken out of his armored suit, he should still pull out some pretty good salvaged tech. And I've always enjoyed the idea that somewhere deep down inside, Lex knows that what he's doing is wrong, but he's so frightened and horrified at the truth of his own monstrousness that he embraces his amoral philosophy all the more.
Doomsday-As others have noted, he lacks the nuances to really be a Big Bad, and is rather uninteresting beyond his physical power. So, to showcase his greatest strength, that of the world's biggest action sequences, he really would have to show up in a Justice League movie as a monster unleashed by someone. Picture the League engaging Darkseid on Apokilips, managing to take the fight to him, with Darkseid being cut off from Earth but still able to unleash a Kryptonian weapon as a spiteful parting shot. Cue an epic battle sequence where the League and the militaries of the world throw everything at Doomsday, but it requires Superman to supercharge himself in the sun and risk burning out to actually stop the monster. Regular rampaging monster just won't do, Doomsday needs to be the type of creature that can take being quadruple teamed by Wonder Woman, Martian Manhunter, Superman, and Green Lantern and still hold the upper hand.
