What I find most confusing is people lauding Alien for it's likable characters while condemning Prometheus for having unlikable ones.
I've never really heard it argued that Alien's characters worked because they were "likeable". They worked because they felt incredibly real and authentic. It really felt like you were a fly on the wall watching a bunch of real-life grunts and blue collar guys going about their job.
Sadly, as much as I enjoyed Prometheus, it's characters come across more like your typical, fake movie types.