The reason I think a female protagonist, or an android protagonist, works so well in a Alien movie has to do with the actual monster, just like I find male protagonists more fitting in a Predator movie. It doesn't have to do with any kind of sexism and gender limits; I'm not saying that either gender, for some reason, is more fit and able to fight the Alien rather than the Predator and vice versa. It's more on a theoretical, philosophical, mythological and archetypical level. It has more to do with perceived femininity, masculinity, androgyny and amorphism.
The Alien is usually referred to as a she or it, whereas the Predator usually is referred to as a he. The Alien represents a nightmarish & amorphous femininity, and mechanical psychosexuality - it's fleshy and mechanic at the same time, it has no ego, it has no feelings or emotions yet it breeds. It's intrusive and invasive. It wants your body to propagate. It's a bringer of life.
The Predator represents beast-like & exaggerated masculinity, and organic asexuality - it's muscular and polished at the same time, it has a big ego, it has feelings and emotions but is figuratively unable to breed. It's unreachable and exclusive. It wants your body for a trophy. It's a bringer of death.
The Predator is a purely masculine, asexual and egocentric killer whereas the Alien is an amorphously androgynous, psychosexual and egoless breeder. One is a polished Greek god from hell, the other is a representation of Mother Earth in the most nightmarish kind of way. They represent two different archetypes.
This is alluring, at least to me, as you're pitting a human archetype against its monstrous counterpart. It turns into a nemesis fight. It represents the endless struggle. David vs. Goliath. So when the protagonist in an Alien movie is either a woman or an android, it works as the underdog equivalent to the Alien, just like a male protagonist in a Predator movie works as the underdog equivalent to the Predator. If you switch the two you theoretically and archetypically get a different dynamic.
A female main protagonist in a Predator movie would technically bring an underlying feminist and anti-patriarcal discourse and dimension to the movie. Revolution against authority.
A male main protagonist in an Alien movie on the other hand would bring an underlying struggle for familiarity and traditional hegemony to the table. Man versus Mother Nature.
Ok... SUPER PRETENTIOUS, I know, but that's my mumbo-jumbo wannabe schoolar analysis on why I rather have female (or android) main-characters in Alien movies and male main characters in Predator movies. With that said, I'm absolutely sure we can break the mold and have excellent male main-characters in Alien movies and vice versa.