Assuming that there's ever a direct sequel to Prometheus, and that's not a given, it seems that it won't be written by Damon Lindelof, and this is despite him already having pitched a follow-up at the same time as his version of the last film.
Collider spoke to Lindelof at a Star Trek Into Darkness press event and came back with quotes on why he's not going to be reuniting with Ridley Scott for more of the same:
...I think what ended up happening was that the movie came out, and there was a reaction to the movie. And I got really wrapped up in Trek, and really wrapped up in this movie that I?m producing and writing with Brad Bird. And I have a TV project that I was really passionate about.Scott has wrapped his next film, The Counselor, and next could be his Blade Runner sequel, The Forever War, more Prometheus or... something else entirely. All we really know about it, whatever it is, is that Damon Lindelof is too busy to get involved with it and it's not like Scott asked him anyway.
Ridley and I had a meeting after Prometheus came out where we started talking again about where this journey would go. And in that meeting I said to him, unfortunately, before he could ask me and go through the discomfort of whether he was going to ask me or not? It?s sort of like having a date where you?re letting the other person know, ?I?m in another relationship.? So I can?t tell you that he asked me and I said no...
...I?m usually very single-minded creatively. I can only be working on one thing at a time. So I said to him, ?I really don?t think I could start working on this movie until I do this other stuff. And I don?t know when the other stuff is going to be done.? And he was like, ?Well, okay, it?s not like I asked you anyways.? He and I are on excellent terms and it was a dream come true to work with him. But much to the delight of all the fanboys, I don?t see myself being involved in Prometheus-er.
I'd like to see more in the Alien universe. I wouldn't even say no to a follow up to Prometheus. I'm just pretty sure I wouldn't want Ridley Scott to be in charge of it.
To Scott, this world is a perfect platform for exploring his "big ideas" about "creation." Unfortunately, those big ideas are completely empty, pseudo-philosophical bunkum. I hope he ends up anchored by better ideas, whether they're big or small, from here on out.