my wife noted, and i agree, that Ripley is quite devoid of any substantial personality, nothing much beyond gender to make us root for her. she wasn't a crummy jerk, so she wasn't unlikable as such, she simply wasn't likable as a fleshed out personality. Kotto & Stanton (and maybe Cartwright) are the characters with the most personalities...we know where they stand...but Ripley? why should we care? (no, really). In Prometheus at least the characters have clear personalities.
You make a good point; Ripley doesn’t have a whole lot of depth in Alien. Most of the characterization goes to Brett and Parker, although you do learn that Ripley is smart, professional, and cool under fire. Alien is really just a story about a woman struggling to survive. It is a suspense/thriller. Any larger themes are subtle.
Maybe my deal with Prometheus is that it just tried to hard. It wanted so hard to explore these large themes of creation, God, myth and death that it just felt too convoluted. This, combined with what I felt were unrealistic & unbelievable characters, left the film hard to get into.