I've been thinking about how to go about a sequel. I know everyone here wants Brainiac, so I've been thinking about what that might look like. My conclusions: the same imagery we've seen from too many films so far. A ship hovering over a city shooting down an energy beam to destroy it (or bottle it in Brainiacs case). We saw that in Star Trek over San Fran (an energy beam drilling down into the Earth); in the Avengers over New York (a blue energy beam opening a portal for an army); and we'll see it in… Man of Steel over Chicago/Metropolis (a blue anti-gravity beam sending everything on the surface upwards). It makes me think everyone wants Brainiac because it's easy to picture, but that's because we've seen it enough times before! It's why the thought of Brainiac in a sequel doesn't excite me at all.
So I've been thinking about what is a natural progression of the story that is worthy of Nolan and Goyer again. This is what I'd like to see…
The continuation and introspection of Superman on Earth. People won't automatically accept and trust Superman just because he stopped Black Zero and Zod. I'd like to see Superman learn his limits in intervening in our affairs. Position Superman as more of a global protector. Have him try and tackle foreign disputes. What we know of MOS, is there will be a strong military presence, but I think the narrative will keep all the focus tight on Zod and not on international conflicts. Here's some imagery that I'd love to see them adapt. It has that same mature, real-world look and relevance to our own economic climate that I can guarantee the Marvel films would never touch. Whilst the Marvel films are great, they are pure fluff.
(Lois getting shot whilst working as a war reporter overseas is a striking image)
Who would be the villain of this sequel then? Who else but Superman's greatest adversary. The one man who will never accept Superman, only hate him to his very core: Luthor. Another take on the 'most powerful man in the world' who will use his influence and power to stop at nothing to reveal Superman as the alien devil he knows he is. Someone who can strategically place Superman into impossible moral propositions and courses of action. Shock Superman to his core. Make him question his very mission and purpose. That excites me far more than Brainiac ever could.
In terms of a 3rd film to conclude the trilogy (all fingers crossed). Think of how Nolan and Goyer approached it with Batman. They took a villain byproduct of the 90s (Bane) and really made it work. For this same reason I really could see them re-think Doomsday the same way (consider too that WB has expressed interest in doing this in the past). Make him a Kryptonian genetically mutated abomination that cannot be killed. My main reason for suggesting this though is this: since they are trying to make the world in these films as close to ours as possible it's just too much that we would make contact with more than one alien species inside a timeframe (thus Darkseid, Mongul, etc.). Just like TDKR came full circle by going back to the League of Shadows, Doomsday could do the same by tying back into Kryptonian lore. It keeps the trilogy tight and self-contained and wraps it in a nice bow. Hopefully something that we can be as proud of as batfans are of the TDK trilogy.