I use a version of an exp system from other games for all my games.
-You showed up. 1 exp.
-You completed a dungeon/story chapter. 1 exp
-Completed a whole story campaign. 1-3 exp depending on its scope.
-You completed a personal character arch. Learning a lesson and growing as a character or dealing with their past catching up to them. 1 exp.
-There was an instance of particularly good rp. Especially if playing true to the character had negative consequences. (I let this be a discusion at the table and have players nominate each other). 1 exp.
-Someone had a particularly ingenious solution to a problem. See above. Its a conversation. 1 exp.
-"heroic moment" or big risk for big reward and doing cool shit in general. Wow moments. This can even be a big betrayal or the pay off for shadowy machinations if thats in the characters nature. Again, conversation. 1 exp.
I might add in extra criteria depending on the game. Like in forbidden lands reaching a new hex is 1 exp.
This system rewards advancement as a group and individual merit for playing what the game is supposed to be.
That being said, an alien rpg cannot focus on the titular xenomorphs. They don't work as ongoing villains because they loose their edge. Like lovecraft stuff the really weird horrifying things need to show up rarely and have massive impact or they suffer from villain decay. At which point... Why are you playing alien?
I plan to ise the game to run a series of one-3 shots that will jump around to different smaller stories and characters to tell a bigger narrative. We will play our regular forbidden lands. Then break it up with a little alien. Then regular FL. Then another seamingly disconnected alien. And eventually a finale alien that ties the other smaller stories together.