Just to clarify some of the confusion, Prometheus is technically a prequel to the Alien franchise but it's also meant to be it's own unique identity. This movie is not a sequel that takes place after the events of Alien: Resurrection but rather what happens after Prometheus.
There is an actual sequel for the Alien franchise coming after this movie and is going to be directed by Neil Blomkamp and it will take place after Alien: Resurrection. We probably won't get in until 2019-2020, though.
