i just think they picked the cute little nostromo because they saw what an armed crew could do. the government (hokaaaahs) didn't want their crew to kill, so they chose a crew without weapons, that couldn't harm, but bring the alien alive to earth, because the prometheus kicked the jockeyship really hard...
and stop complaining: a movie from 1979 can't look more advanced than a movie from 2012, of course in ALIEN they had those old pcs and shit, ignore this and try to make Prometheus as "logical" as possible, because Scott has the tech and the money for that, which isn't a bad thing if yoĆ¼ correct those little details...