I doubt it. Neill's not really a "hired gun" director. Everything he's done has been a passion project he built from the ground up, including Alien V, despite it existing in an established universe. Fox didn't bring Alien V to him, he brought it to Fox. Prometheus 2 is already kind-of in pre-production (there's a script, or at least a draft of a script), and I really doubt Neill would just sign on to a project like that unless he really wanted to (and had permission to) play around with it and make it entirely his own.