My sequel theory:

1) The military (and heck, everyone else) will be freaked out that a Kryptonian is still living on Earth. After all, look what those Kryptonians did to Metropolis and the Indian Ocean! Billions of dollars of property damage and hundreds of thousands of lives lost.

2) The military and the civilian powers: "We can't do anything to stop this guy." (as was so graphically shown in the movie.) "We need to find something that will hurt him so that we are not helpless if this Superman guy goes rogue. Yeah, he says he's a friend right now, but what if he doesn't stay friendly?"

3) Lois Lane mentioned that the World Engine was making things more like Krypton, where Superman wouldn't have powers/abilities. I think she might have said this in front of some military guys. "Maybe we should go look at the debris from where the World Engine was and see if anything there will affect Superman."

E.g, I can see KRYPTONITE being invented in this movie universe.

4) "We'll investigate it from a military point of view" say the generals. "But we need some scientific guys looking at things too. They should investigate that World Engine, and the spaceship wreckage, and the remnants of Metropolis that got crunched by the gravity waves. Gee, doesn't LexCorp have a R&D division? And how about Wayne Industries? And what about all the universities and think tanks out there? After all, our species was nearly destroyed. We've got to learn more so this doesn't happen again!"

Meanwhile, Lois and Clark will be working together at the Daily Planet. Clark won't stay a stringer for long (or will he? Interesting plotbunny there.) They'll have a slowly-increasing romance at the same time they're writing stories about the rebuilding of Metropolis. Lois will be using her sources to check into the investigation of what makes Superman vulnerable. However, her investigation will be hampered, because everyone will be surveilling her because they know she knows Superman's civilian identity.

So... I can see a huge effort at trying to understand Kryptonian technology. Kryptonite (or maybe red sun radiation) will be discovered. Somehow Superman will be found to be vulnerable to it. He will get into trouble. Lois will have to save him somehow.

I'm still debating the ancillary events, like, "Will Perry find out that CK=SM?" "Will Jimmy Olsen show up?" and, importantly, "Will Lois and Clark achieve physical intimacy?"