Well, here's what i think could be interesting answers to those questions....What is Meredith Vickers’ Alternate Agenda?
Who is the second Andriod?
I believe Vickers' real agenda is to gain control of the Company from her father, who she has become less attached to since the creation of David.
What are in the ampules? What role do they play?
David 8. Who I believe we may see several times.
What were the murals changing into?
They contain the DNA source of thousands of species across the galaxy, a catalogue of the numerous species the Engineers helped to evolve.
What happened to the Engineers? Why are they all dead within the temple?
They are our equivalent of 3D pictograms that change shape in order to communicate a tell.
Scott says the mission can be described best as a “challenge” to the Gods. If the Engineers are the gods, how do we challenge them?
Their latest creation (the Hammerpede) designed to protect the Ampule Room, turned against the Enginneer's causing most to abandon the waystation.
Why is the Juggernaut going to Earth? Who are ‘they’?
Weyland believes this 'invitation' was a challenge the Gods (who we haven't seen yet) had set the Engineers, and is now bestowed upon humans to succeed where they had failed, but it's the rewards he's really after for himself.
Is Peter Weyland on board? (Prometheus)
I don't think the Juggernaught is going to Earth, rather the Last Engineer attempts to reach others of his clan, which could lead to invasion because of what we know.
How does Holloway & Vickers die?
Yes definately, other than the Engineer's this story is mostly about him.
What is the purpose of the giant face/head?
I think Vickers survives the whole thing. Hollway becomes a mutant Engineer, killed later on either by the Squid Shaw gives birth to, or (most likely) the woman herself.
Three Engineers – Last, Ghost, and Sacrifice – who are they and what is their purpose?
I still believe the Giant Head might really be 'alive' and function as part of the Juggernaught. I also find it curious we've never seen the Juggernaught from the front yet.
What can we expect from the xenomorphs? What will be the connection in the last 8 minutes?
1) Sacrifice is the Engineer we know about
2) Ghost is from the hologram I believe tells their tragic story
3) Last is one of a few left behind (for whatever reason) but survived.
What is Shaw sorry about?
I don't think we'll see anything from the original film or any direct connection to Alien, but I do believe the last 8 minutes could well feature a face-Hugger variant.
How do the survivors get back home/off the planet/all die in the end?
Shaw is a believer who now feels responsible for persuading others to believe in what they were getting involved in resulting in their deaths.
What are the stages of the new alien creature? Are there four or more? What are they?
Shaw and Vickers are rescued by a company vessel, then all hell breaks lose with a final showdown against the Hugger variant who gets on board, only Shaw and Vickers survive the outcome.
Why did the Engineers create us in the first place?
1) Shaw gives birth to a snake-like creature.
2) Later this becomes a giant Squid-like creature with many arms and tentacles.
3) In one last recognisable change it becomes a Hugger variant able to "face rape" multiple hosts.
I think the Engineers merely accelerated our evolution on Earth, a task they performed on countless worlds as a tribute to their Gods who (perhaps) had sinister intentions, only for an Engineer called Prometheus to emerge as our saviour for reasons we already know about!
(Note: some questions I wasn't sure of and added my own interpretation of and may be wrong)