Things we're probably going to find out.
1. The SJ ship is a terraforming vessel/bomber. The cargo is used to wipe out any indigenous lifeforms and then the terraforming begins.
2. Humans were created to serve as SJ workers/slaves on a terraformed Earth.
3. The SJ's are neither good nor evil.
4. There are many planets where the SJ's have left behind "temples" and bio weapons.
5. The xenos are a creation of the SJ's.
6. Weyland is an crazy old man hellbent on achieving godlike status/live forever.
7. Shaw will give birth to something.
8.SJ's or their creations will kill crewmembers, perhaps after Weylend tries to steal thier tech.