Just to bring things back to the harsh light of reality...
In "Close Encounters of the Third Kind", the motivations of the extraterrestrials may have remained a bit nebulous and uncertain...but the motivations of the friggin' humans were NEVER unclear, uncertain, confusing, or required a further sequel to explain. Furthermore, the inscrutability of the "CE3K" aliens left things actually interesting, and something to ponder.
IMHO, with CE3K, we have a masterpiece...one for "ages", as it were. With Prometheus, we have a film that will be shown on the SyFy network next year. I very much doubt (again, IMHO) that anyone will be talking about it 30+ years from now.