Skulls equal to; A.I, Muthur, Ron Cobb Spaceships, Synthetics, W-Y, Seegson, USCM, USM, (Unusually long) Cryosleep, Shake and Bake Colonies, Engineers, The Pathogen & even more!
As for Prometheus- well, there you go- bill it as the Prometheus series then.
Or Black Mirror.
Or Mad Max, none of those entries are directly connected and
apart from the first film Max isn't the driving force of the plot-
he gets caught up in it.
There's lots of ways to do Anthologies.
I'm not a proponent of ditching the Alien altogether, just like I'm not a proponent of ditching the Alien Queen.
But you don't need either 100% of the time. Especially with the universe Alien set up beyond the monster.