My current thought for Alien is to not tell the players that we're playing the Alien RPG. I might just say were using some similar rules as Forbidden Lands in a homebrew sci-fi setting and spend most of the sessions dealing with various underworld figures, competing smugglers, and law enforcement types. Once there nice and comfortable with the expectations of the setting it will be time to throw them for a loop. Maybe a smuggling job transporting xenomorph pods goes awry, or they return to a familiar orbital station that appears completely abandoned, or maybe they're attacked by something like the reavers from Firefly hosting alien parasites in their degenerate minds!
I'm not completely sure yet, but I definitely want a slow build to the realization that they are playing Alien!
I really like this idea! Not only because a space underworld would be really cool, but also because it's a new and creative take on Alien. As you suggest, it might be a way to use xenomorphs in a new way. I would also add The Company in some form. I imagine they, or at least some of their staff, must be working with (and against) several crime syndicates that might be operating in space. It should be possible to scenarios tat are space heists or tech noir in some form. In my eyes, new genres is a way to develop the Alien franchise. Hopefully I will soon post some ideas about the space underworld in another, new thread!