I want them to address the os issue. Because that's the one thing everyone has to say about this issue. I want them to try it again but hit a firewall, or at least have someone bring it up and get laughed out of the room.
And I want to feel like we're really living in a different world, because we would be. Not only do we know for sure we aren't alone in space, but a good chunk of the world was blown up. We don't really get much view of the other countries, but all the important American politicians except the president were killed. Rebuilding under the new world with a power vacuum and under a curtain of fear is some really heavy stuff. The power balance is going to be very different from what we know.
And even though we didn't fully understand their technology, it's going to have some sort of influence on our technology. Some degree of it will bleed into the military and then out into the private sector. They'd probably figure out a way to get shields and energy weapons of some sort.
And I'd also like to see what tabloids look like now. Will there be more "space aliens stole my face!" stories, or less? Will we start to worry about robots instead? Will people who claim to have been abducted be treated with more reverence (or at least not as utter psychos)? Will we have a Men In Black type agency that goes around investigating to sort out the true encounters from the drunken hallucinations?
Has earth gained some sort of interstellar reputation? Were those the only aliens, or are there others? Do they respect the way we stood up for our planet or despise us for our failure to effect a democratic solution?
Has culture on the alien planet changed as well? Will they come to us in apology, only to be met with scorn, suspicion, and an attempted hacked computer virus? Are we the aggressors this time?
And as much as I hate sequels where the main characters from the first are just cameos, I think enough time has passed that that's the only way this could really work. If it's the same people, I think we're going to get something too close to the same story over again, and that would be worse. They should only be around in an advisory capacity.
The romance was handled well in the first one. I really feel like they're going to mess it up this time. I liked that Jeff Goldblum and his ex-wife didn't really get back together in the end. I don't want to find out they got remarried and are going through the same crap again. I don't want any extraneous love interests or damsels in distress. Romance should stay in the background and have something to add to the story.
And go easy on the CGI. Only use it if you need it.