I think that the Alien films are much deeper. They're about human exploration, and about going into the unknown. But ultimately they are about discovering the roots of our demise, and consistently, in every film, those roots are... wait for it... ourselves. In every Alien film, the worst monsters were the people and their creations. The prequels come full circle in that now it's our creations' creations which have the potential of our demise. It's heady stuff.
But importantly, as I said above, it's in the subtext. These issues are not overtly dealt with, but they are under the surface, which is very elegant. Are they deeply philosophical films dressed up as horror flicks or the other way around? I don't know. But at least the question is valid. Can you say the same about the Predator films?