Agree with you, BobJM, that Lois should be showing him the ropes as a reporter. As far as we know, he neither any training, experience, or education in the field.
I'd really like to avoid the the Lois-wants-him-to-use-his-powers-for-her-story thing. I dislike that idea intensely. Lois is very, very good on her own.
I can't decide if it would be amusing or annoying to have someone else see his lack of experience and wonder how he got the the job.
Obviously follow-up on the subset of the population that rejects Superman, those that might blame him for drawing Zod here, would be good to me. I'm not sure how I want Lex to play in in that. I mean, him using anti-Superman sentiment, even whipping it up further, seems quite feasible to me, given the themes of MOS. But they really gave Zod a motivation, a reason, for his nature, his actions. So what is Lex's reason for what he is doing - why does he hate Superman? What does he gain from destroying him? If they go the scienc-y route with Lex, would the codex in Superman's blood be of use to him?
As for any potential anti-Superman sentiment - I'd like to see that the DP made sure they put out Superman as hero. Because he is, of course. And Lois knows that he gave himself up and how he did this to save them at the expense of his own people being reborn. Not sure how much of that will be publicly available - what would Perry allow to be published? Unlike the beginning of the movie, the public is now willing take seriously anything Lois might write about it. It will be interesting how much the DP shapes pubic opinion on Superman. And how do the other DP staffers feel about him? Of course, this aspect on how soon after MOS a sequel picks up.
I am fervently hoping there is no mindwipe of Lois - and I don't think there will be. But a tiny part of me still worries, given her history. I want to see more of the Lois/Clark dynamic, of them learning more about each other. But we can't see all that, of course, because there's only so much time in a movie. Some of it will have to alluded to or implied. Or have already happened off-screen, between movies. But I'd like to see some, and some of the two of them being reporters - perhaps as a lead-in to a plot-point or action scene. I don't want really-dweeby Clark. I always liked the Clark-as-the-real-guy version. Well, most of the real guy, anyway. That way he can have real relationships, friendships, etc. But, since Lois does know the truth, he can already have that relationship, even if he plays the dork. But it they go that way I so want Clark and Lois to rehearse/try-out some of the dorky bits as a humorous scene.
How does Perry treat Lois in the aspect of her potentially knowing Superman's identify? Does he want to publish it? Or want her to consider it? No, I think he knows she won't (phone conversation in MOS), but how does he feel about it? Think it's just being a responsible journalist? And will we get some implication that he's a smart enough journalist himself that he can put those pieces together and see that it's Clark (but never tip his hand to them)?
Emotional issues over having had to kill are likely to plague Clark. I don't want that to overshadow everything else, but as a recurring theme and part of a larger whole, it could work well.
Lastly, I guess, I want to see how Clark reacts to having a permanent place. It seems he was a traveler before, he didn't forge new connections of any depth. He always had to ready to walk away a moment's notice, as soon as something happened? Now we the issue that he can put a costume and then go back to work afterwards. Does he maybe consider running when something happens? He is using his real name now, and I don't think he was before (he definitely wasn't as "Joe", but Lois' talk about tracking him down indicate he wasn't the other times, either, I think). I don't think running will come up - I think he's past that. But maybe. It's just an interesting thought, how making himself a permanent place might effect his non-Lois, non-Mom relationships.