Loose ends in the Alien franchise don't bother me that much.
There is little connection story wise between "Alien 3" and "Resurrection" beyond it's Ripley's DNA, xenomorphs are still around 200 years later & scientists still want to experiment on them to create super soldiers.
And the end of "Resurrection" was never continued.
The film is very self contained.
I see the prequels in a similar way. They are a two part self contained story in the Alien universe.
Only they do a decent job in adding to the viewer's knowledge about this universe in terms of the Space Jockeys as well as the Weyland Corporation who both set the stage for the events in "Alien".